This is the accepted version of the article:
Jarad, Mai; Antoniou-Kourounioti, Rea; Hepworth, Jo; [et al.]. «Unique and
contrasting effects of light and temperature cues on plant transcriptional pro-
grams». Transcription, Vol. 11, issue 3-4 (Oct. 2020), p. 134-159. DOI
10.1080/21541264.2020.1820299
This version is available at https://ddd.uab.cat/record/236811
under the terms of the license
UNIQUE AND CONTRASTING EFFECTS OF LIGHT AND TEMPERATURE CUES
ON PLANT TRANSCRIPTIONAL PROGRAMMES
Mai Jarad1, Rea Antoniou-Kourounioti2, Jo Hepworth2, Julia I. Qüesta1
1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB,
Bellaterra, Barcelona, Spain.
2John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
Corresponding author: julia.questa@cragenomica.es, jo.hepworth@jic.ac.uk, rea.antoniou-
kourounioti@jic.ac.uk
1
ABSTRACT
Plants have adapted to tolerate and survive constantly changing environmental conditions by
reprogramming gene expression in response to stress or to drive developmental transitions.
Among the many signals that plants perceive, light and temperature are of particular interest
due to their intensely fluctuating nature which is combined with a long-term seasonal trend.
Whereas specific receptors are key in the light sensing mechanism, the identity of plant
thermosensors for high and low temperatures remains far from fully addressed. This review
aims at discussing common as well as divergent characteristics of gene expression regulation
in plants, controlled by light and temperature. Light and temperature signalling control the
abundance of specific transcription factors, as well as the dynamics of co-transcriptional
processes such as RNA polymerase elongation rate and alternative splicing patterns.
Additionally, sensing both types of cues modulates gene expression by altering the chromatin
landscape and through the induction of long non-coding RNAs (lncRNAs). However, while light
sensing is channelled through dedicated receptors, temperature can broadly affect chemical
reactions inside plant cells. Thus, direct thermal modifications of the transcriptional
machinery add another level of complexity to plant transcriptional regulation. Besides the
rapid transcriptome changes that follow perception of environmental signals, plant
developmental transitions and acquisition of stress tolerance depend on long-term
maintenance of transcriptional states (active or silenced genes). Thus, the rapid
transcriptional response to the signal (Phase I) can be distinguished from the long-term
memory of the acquired transcriptional state (Phase II – remembering the signal). In this
review we discuss recent advances in light and temperature signal perception, integration,
and memory in Arabidopsis thaliana, focusing on transcriptional regulation and highlighting
the contrasting and unique features of each type of cue in the process.
KEYWORDS
Light and temperature sensing; plant transcriptional regulation; chromatin dynamics; long
non-coding RNAs; epigenetic memory; stress memory
2
1. INTRODUCTION
1.1 LIGHT AND TEMPERATURE CUES INDUCE STRESS AND DEVELOPMENTAL
RESPONSES IN PLANTS
Plants are constantly exposed to varying environmental cues that drive their growth and
developmental processes. Some of the more prevalent abiotic stresses that plants are
subjected to are drought (water scarcity), flooding (water overload), soil salinity, harmful
radiation, toxic compounds in the soil, severe temperatures (freezing, cold, heat), and light
fluctuations. Among them, light and temperature interact to control the timing of all the
transitions of plant development, from germination, through the juvenile and floral
transitions, to seed set and senescence.
Light may vary in intensity and wavelength and, like temperature, fluctuates widely in both
predictable patterns (photoperiod) and unpredictable ones (cloud cover, shading from other
plants). Plants have evolved the capacity to perceive all these complex combinations of light
and temperature cues and utilise these signals to adjust their response. For instance, in the
Brassicaceae and some winter cereals, spring flowering requires the combination of
appropriate day length, memory of past prolonged low temperatures (vernalisation), and
recent warm temperatures (thermomorphogenesis) 1–3. Thus, the intertwining of both light
and temperature sensing, together with the underlying signalling pathways, allow plants
access to vital information that affect their growth and developmental responses. In addition,
plants have developed mechanisms to counteract exposure to harmful radiation and to
extreme temperatures, driving stress acclimation responses for survival.
Perception and integration of light and temperature signals, both developmental triggers and
stressors, result in transcriptional reprogramming. Decades of work has deciphered
numerous Transcription Factors (TFs, activators and repressors) that are responsive to light
and/or temperature. However, recent efforts have started to shed light into other players
such as the chromatin landscape, non-coding transcripts and components of the
transcriptional machinery. In this review, we summarise the different levels of transcriptional
regulation in plants and discuss how they can be affected by light and temperature cues. Our
aim is to highlight common and distinct features of light and temperature mode of action on
transcriptional regulation control in plants.
3
1.2. TRANSCRIPTIONAL REGULATION IN PLANTS
In eukaryotes, transcription of mRNAs, long non-coding RNAs (lncRNAs), miRNA precursors
and enhancer RNAs (eRNAs) start with recruitment of the RNA POLYMERASE II (RNAPII) to
proximal or distal regulatory regions of genes (promoters and enhancers, Figure 1, 4–6). RNAPII
recruitment and assembly at gene promoters located in chromatin accessible regions of the
genome (Figure 1A) is generally facilitated by sequence specific TFs, as well as the regulatory
role of enhancers (Figure 1B). In turn, binding of these “pioneer” TFs may also increase
chromatin accessibility for RNAPII recruitment, and thus a feedback mechanism between
chromatin and TFs is established. Once engaged, RNAPII switches to transcriptional
elongation moving along the gene body (Figure 1C), the nascent transcript is co-
transcriptionally spliced (Figure 1D), and transcription is terminated upon cleavage and
polyadenylation at the 3’ end of the gene (Figure 1E). Although research on transcriptional
regulation has mostly focused on TFs triggering transcriptional initiation (Figure 1B), detailed
mechanistic studies have revealed that transcription consists of multiple regulated steps
including RNAPII pausing and stalling along genes, splicing, cleavage and polyadenylation 7.
The degree of chromatin accessibility adds another level of regulation, influencing not only
TF binding dynamics 8 but also efficiency of the co-transcriptional processes such as splicing
9. Together, these mechanisms determine the speed of transcript production, as well as the
epigenetic state of genes: ACTIVE (ON) or INACTIVE (OFF) 10. Post-transcriptional mechanisms
including transcript stability, nuclear export and inactivation by RNA silencing pathways (for
example the miRNA pathway) will determine transcript fate.
Plant transcriptional responses to environmental threats mostly happen rapidly and
transiently upon sensing of the triggering signal. Initial perception is integrated into signalling
pathways that confluence in the induction of a set of pioneer TFs. The function of those TFs
is to reprogramme the transcriptome by activating or repressing genes (transcriptional
activators and repressors, respectively). However, plant acclimation to stress and induction
of developmental transitions require that the transcriptional status acquired by specific genes
(ON or OFF) is maintained for prolonged periods of time even in the absence of the triggering
signal. Epigenetic mechanisms, such as DNA methylation and histone post-translational
modifications, have the capacity to lock genes in either the ON or OFF state, and perpetuate
these states through DNA replication and cell divisions 11–14. In the following sections we will
4
discuss the impact of light and temperature on different levels of transcriptional regulation,
transiently and long-term.
Figure 1. Transcription in eukaryotes
A, Chromatin accessibility affects the ability of the RNA Polymerase II (RNAPII) and other
proteins to transcribe genes. B, RNAPII is recruited to the gene by transcription factors at
promoters and enhancers for transcription initiation. C, RNAPII can stall at gene boundaries.
5
After release from promoter-proximal stalling, there is transcriptional elongation and 5’
capping of the nascent transcript. The chromatin is directly affected by the activity of the
RNAPII through changes in supercoiling ahead of and behind the polymerase. D, Splicing
determines the sequence of the transcript, and often alternative transcripts can arise from
the same gene as a result of this process. E, The transcript is released from RNAPII by cleavage
and the template-independent Poly (A) Polymerase polyadenylates its 3’ end.
2. LIGHT AND TEMPERATURE CONTROL OF TRANSCRIPTION FACTORS
Light and temperature sensing triggers a cascade of transcription factors that control growth,
acclimation and other responses. Many of these downstream factors are common to the two
signals, thereby facilitating integration of environmental information. Furthermore, some of
the photoreceptors have recently been found to also be sensitive to temperature. In the
following sections we describe the known receptors of the two signals and the downstream
pathways that control signalling, highlighting the interconnections between them.
2.1. LIGHT-TRIGGERED TRANSCRIPTIONAL RESPONSES
2.1.1. PLANT PHOTORECEPTORS
Relatively few reactions are light-sensitive within the spectra and intensity of light at the
Earth’s surface. Therefore, in order to sense light, plants have evolved to produce specific
receptors for light of different wavelengths, most of which require a light-sensitive cofactor
molecule for their activity. Five families of photoreceptors are known to date in Arabidopsis:
the phytochromes (far red and red light), the cryptochromes and members of the Zeitlupe
protein family (both blue and UV-A), phototropins (blue, UV-A and UV-B) and the UV-B
photoreceptor UVR8 (Figure 2).
The phytochromes form a family of five proteins, phyA-phyE, whose activity depends on the
light-responsive, wavelength-reversible conformation of a bilin cofactor. In the case of phyB,
red light switches the phytochrome from its nascent inactive form (Pr) to its active form (Pfr)
while far red light reverts Pfr to Pr again. In the active form, phytochromes move from the
cytosol into the nucleus to mediate their effects through interaction with other proteins,
6
including other photoreceptors such as cryptochromes 15,16. Although they are partially
redundant, the different phytochromes react differently to control distinct responses
depending on light intensity, wavelength and their reversion dynamics 16,17. For example, in
phyB, the active form ‘relaxes’ back to the inactive form in the absence of red light. This ‘dark
reversion’ is temperature-sensitive, giving phyB the properties of a temperature sensor in
conditions with low red light 18,19.
Like the phytochromes, the two cryptochromes are partially redundant. They require a flavin
adenosine dinucleotide as cofactor. When activated by light, the cryptochromes undergo
conformational change and protein homo-oligomerisation to activate binding to targets,
which, like the phytochromes, includes direct interaction with target TFs 20,21.
Phototropins are serine/threonine kinases that also have flavin chromophores, binding flavin
mononucleotides through two LIGHT, OXYGEN OR VOLTAGE (LOV) domains. Unlike the other
photoreceptors, which are nuclear or cytosolic, the two phototropins are plasma membrane
targeted, though not integral membrane proteins. Photoactivation by blue, UV-A and UV-B
light results in autophosphorylation and phosphorylation of target proteins, leading to
movement responses at the intracellular (chloroplast movement), cellular (stomatal opening)
and whole plant level (phototropism) to maximise light reception 22,23. In common with
Arabidopsis phyB, the phototropins have also been implicated in temperature sensing (see
thermosensors section).
A single LOV domain is present in the Zeitlupe family of three flavin-binding proteins: ZTL
itself, FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (FKF1) and LOV KELCH REPEAT PROTEIN 2
(LKP2). All three mediate blue light clues to the circadian clock via their F-box domains as part
of E3 ubiquitin ligase complexes, marking target proteins, such as CYCLING DOF TFs, for
degradation 24–26.
Most recently discovered is the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) 27,28.
Ultraviolet photon absorption by UVR8 causes monomerisation from the inactive homodimer
29 leading to translocation to the nucleus and interaction with CONSTITUTIVE
PHOTOMORPHOGENIC 1 (COP1) 28,30. Uniquely, UVR8 does not require a chromophore
7
cofactor, with light sensitivity being provided by tryptophan residues within the protein itself
31.
In addition to these dedicated receptors, light reactions in the chloroplast lead to
transcriptional responses both within the chloroplast itself and, by a variety of retrograde
signalling pathways, in the nucleus. These signalling pathways include the direct outputs of
photosynthetic function such as reactive oxygen species (e.g. single oxygen) 32,33, metabolites
required for chloroplast function such as tetrapyrroles 34, and proteins from both nucleus and
plastid, including transcription factors such as PHD-TYPE TRANSCRIPTION FACTOR WITH
TRANSMEMBRANE DOMAINS (PTM) and the integrator TF ABSCISIC ACID INSENSITIVE4 (ABI4)
17,35–39. Moreover, as the reactions of photosynthesis are inherently heat-sensitive, this
retrograde signalling is also linked to temperature responses 40,41. Similarly, circadian
dynamics are a vital part of the modulation of light and temperature signalling, and are also
controlled by light (e.g. the Zeitlupe family) 42,43.
2.1.2 TRANSCRIPTION FACTORS IN THE PRIMARY RESPONSE TO LIGHT
Light inputs from three of five photoreceptor families converge on the activity of a small
number of transcription factors (Figure 2). In particular, two families of TFs dominate light
responses: the basic Helix-Loop-Helix (bHLH) PHYTOCHROME INTERACTING FACTOR (PIF)
family and the basic ZIPper (bZIP) TFs ELONGATED HYPOCOTYL5 (HY5) and its orthologue HY5
HOMOLOGUE (HYH). Light-induced changes in PIF and HY5 activity act through relief-from-
repression mechanisms at different stages of the transduction route. Both families are key to
plant development, particularly photomorphogenesis. Most information on light signalling,
retrograde or otherwise, has been derived from study of this process, in which seedlings
undergo major transcription, cellular and morphological changes from an autotropic etiolated
‘soil-grown’ state to green, phototropic, open-cotyledon phase.
HY5 and HYH generally act partially redundantly to promote transcription in response to red,
blue and UV light signalling (Figure 2). HY5 itself lacks a transcriptional activation domain, and
recent work has further supported the hypothesis that HY5 relies on interacting TFs to
upregulate its targets, which trigger a cascade of indirect transcriptional responses 44. In the
dark, HY5 and HYH, along with several other factors that promote photomorphogenesis, are
8
ubiquitylated and marked for degradation by the 26S proteasome, through the action of the
master light integrator, the E3 ligase COP1-SUPPRESSOR OF PHYA-105 (COP1/SPA) complex
45–47. COP1-SPA complex action is in turn inhibited by the binding of activated (Pfr)
phytochromes and cryptochrome oligomers to SPA proteins, resulting in the stabilisation of
HY5 in the light and promotion of photomorphogenesis 17,20. Active UVR8 monomers also bind
to COP1 in the nucleus in a light-dependent manner, outcompeting COP1 binding of HY5
27,28,30,48. Although several different photoreceptors converge on HY5 via COP1, they do so in
different manners and have different effects. Unlike PIF and CRY signalling, UV-B requires
COP1 as a positive factor 49, with the resulting stabilisation of HY5 mediated through interplay
between antagonistic E3 ligases downstream of UVR8 action 50. UVR8 also binds to WRKY
DNA‐BINDING PROTEIN 36 (WRKY36) to inhibit its binding to and repression of the HY5
promoter, resulting in increased HY5 transcription 51. In turn, CRYs antagonise UVR8
responses over the light spectra that both receptors share 52. HY5 also directly promotes
expression of its negative regulators COP1, SPA1 and SPA4 in a negative feedback loop 44.
The PIF family are key pioneer TFs for light signalling with critical roles in plant development,
integrating light responses with temperature, hormone signalling and circadian dynamics
16,17. In contrast to the HYs, PIFs act as negative regulators of photomorphogenesis by binding
to G-box motifs in target promoters, antagonising HY5 action at shared targets 53. In the dark,
PIF proteins are stabilised by the binding of COP1 (PIF3 and PIF5 54,55) and DE-ETIOLATED 1
(DET1 56). DET1 is a classic negative regulator of photomorphogenesis, like COP1, and similarly
provides substrate specificity to a CULLIN4 E3-ligase complex 57–60. PIF repression of
photomorphogenesis is relieved in light by phytochrome-triggered phosphorylation and
degradation of PIFs, by the action of phyB in reducing PIF1 and PIF3 binding to DNA at target
promoters, and by UVR8-mediated reduction in COP1-PIF5 binding, leading to PIF5
destabilisation 16,61–65. Although partially redundant, different PIFs have different affinities
for the various phytochromes, particularly the ‘light labile’ phyA, and for different
heterodimerisation partner TFs 16,17,66. As well as their interaction with phytochromes, CRYs
also interact directly with PIF4 and PIF5 at the chromatin in limiting blue light and repress PIF
transcriptional activity in high temperature responses 67,68.
As well as the PIFs and HYs, all the photoreceptors, except the phototropins, are known to
interact directly with other TFs to mediate their specific responses. As a few examples: phyB
9
triggers the light-dependent degradation of EIN3 to reduce ethylene signalling 69. UVR8, CRYs
and possibly phyB interact directly with transcription factors such as BRI1-EMS-SUPPRESSOR
1 to integrate light signalling directly with the brassinosteroid signalling cascade 70–72.
Separately CRY2 binds with CRYPTOCHROME‐INTERACTING bHLH1 (CIB1) to directly promote
FT expression and flowering 73, while varying effects on flowering time due to different
degradation targets characterises the separate members of the Zeitlupe family 74. Some of
the protein-protein interactions in these pathways may also be directly temperature sensitive
75. As well as WRKY36, UVR8 also functions in root development via association with MYB73
and 77 76.
In summary, although the various photoreceptors have distinct roles in development, they
overlap in both their spectral sensitivities and target TFs. This results in a complicated
crosstalk in natural, multispectra light conditions, which provides plants with the possibility
of fine tuning their responses. Moreover, both photoreceptors and their interacting TFs
additionally have roles in mediating temperature responses.
10
Figure 2. Multiple light signalling pathways are sensed by receptors and converge on
transcription factors in the nucleus.
From the left, UV-B is received by UVR8 and triggers its monomerisation, association with
COP1, and movement to the nucleus, which results in TF binding and HY5 stabilisation.
Phototropins (blue, UV-A and UV-B) sit at the plasma membranes and light triggers their
kinase activity. The members of the Zeitlupe family (ZTL, FKF1, LKP2) respond to blue light via
changes in their affinities for different protein cofactors and their E3 ligase activity to affect
the circadian clock (three-arrow circle), which has effects at all levels of cell activity, including
the activity of PIFs. Blue and UV-A are sensed by CRYs, resulting in oligomerisation and TF
binding in the nucleus as well as HY5 stabilisation. Phytochromes are activated and
deactivated by red and far red light and respond by moving to the nucleus, destabilising PIF
TFs and preventing PIF DNA binding. From the right: light fluence and quality activates the
photosynthetic machinery, and results in biogenic and stress responses, communicated to the
nucleus by a variety of routes. These include the cleavage of the chloroplast-envelope bound
PHD transcription factor PTM, which moves to the nucleus itself to effect transcriptional
responses. Key: Light split by a prism enters the cell (pale yellow rounded box), pale blue
rounded box: nucleus, pale green rounded box: chloroplast. Lightning arrows: effect of light
activation. Solid arrows: protein movement. Dotted lines: processes including multiple
metabolites & proteins. Policeman black/white: COP1 active/inactive. Rectangular boxes in
nucleus, grey/orange/green/white: TFs, HY5/PIFs/cleaved PTM/unspecified. Photoreceptors
in thick black outlines are also defined as thermosensors.
2.2. INFLUENCE OF TEMPERATURE ON TRANSCRIPTIONAL INITIATION
2.2.1 PLANT THERMOSENSORS
A thermosensor detects changes in temperature cues by inducing changes in its structure
and/or activity to adapt to the perceived signal. At the same time, temperature affects
multiple processes in the plant and appropriate coupling of these temperature sensitivities
can lead to compensation77 or amplification78 of the signal. As a thermosensor stands at the
11
core of any thermosensing mechanism, identifying specific thermosensors has been the
target of much research effort 79.
Temperature fluctuations are known to affect cellular membrane fluidity, which in turn
affects the activity of membrane bound proteins as well as their structure 80. These changes
in membrane fluidity are speculated to be the first step in the thermosensing process. Ca2+
channels are membrane bound proteins that exhibit changes due to cold temperatures,
triggering Ca2+ influx. This influx is probably sensed via the Calmodulin Binding Transcription
Activator (CAMTA) family of TFs to govern expression of the cold-responsive C-REPEAT
BINDING FACTOR (CBF) genes. However, as of yet, there is no clear explanation of how Ca2+
influx is regulated under cold stress 81–84. Heat stress has also been shown to affect Ca2+
channels and swiftly trigger Ca2+ influx to induce thermotolerance 85,86. Further
characterisation of the role of Ca2+ channels in the thermosensory mechanism will be needed
in order for them to be considered as thermosensors themselves.
Temperature fluctuations affect protein activity and/or structure, therefore thermosensing
can occur through protein conformational changes under the influence of temperature. A
good example is phyB. Red light induces the transition from active Pr to inactive Pfr by altering
the structure of its chromophore, with warm temperatures inducing the relaxation of the
chromophore back to the Pr state18,19. Other phytochromes have also been proposed as
thermosensors since it has been observed that temperature-induced hypocotyl elongation in
the quintuple phytochrome mutant (phyabcde) is lost 18,19. In addition, the blue-light
photoreceptor phototropin has been shown to sense cold signals in the liverwort Marchantia
polymorpha through its temperature dependent reversion dynamics, and is required for the
cold-avoidance movement of chloroplasts 87,88. This temperature sensitive role may be
mediated by PHOT2 in Arabidopsis88. Further investigation is required to determine the
viability of phototropin as a thermosensor in plants.
Moreover, high temperatures can lead to protein misfolding. Under the influence of high
temperatures, HEAT SHOCK PROTEINs (HSPs) bind misfolded proteins, triggering in turn the
release of HEAT STRESS TRANSCRIPTION FACTORs (HSFs) that regulate the thermotolerance
response through a set of HEAT STRESS RESPONSIVE (HSRs) genes 89,90. In addition to proteins,
RNA molecules can also be sensitive to conformational changes upon temperature variation.
Recent work has provided an example of an RNA thermoswitch in plants. The 5’-UTR of the
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PIF7 RNA folds into a hairpin structure, which adopts two distinct conformations in a
temperature-dependent manner 91. This molecular switch adopts a more relaxed, yet distinct
conformation at warmer temperatures, resulting in enhanced translation.
Pioneering work on the effect of temperature on chromatin dynamics proposed the histone
variant H2A.Z as a potential thermosensor 92. In Arabidopsis thaliana, nucleosomes containing
H2A.Z are evicted from chromatin as ambient temperature rises 92. The question of whether
temperature could directly affect H2A.Z nucleosomes remained open for several years and
led to much speculation. However, follow-up work demonstrated that H2A.Z nucleosome
eviction requires the function of the HSFA1 clade of the Arabidopsis HSFs 93. Indeed, in
Brassica rapa, a close relative of Arabidopsis, H2A.Z controls transcriptional response to
temperature but in the opposite direction, as H2A.Z levels increase with increasing
temperature 94.
A new physical mechanism of temperature sensing has recently been described, whereby the
relative abundance of a protein changes in response to temperature, but without an
equivalent change in expression or stability. The transcription factor NTL8 accumulates over
long periods of cold through a dilution-mediated mechanism, due the temperature-
dependence of growth 95. Whether similar mechanisms underlie other temperature
responses is unknown. Despite this recent progress, plant thermosensors, unlike light
sensors, remain largely uncharacterised.
2.2.2. TEMPERATURE-RESPONSIVE TRANSCRIPTION FACTORS
Several signalling pathways have been proposed to regulate cellular responses to both
elevated and low environmental temperatures. Heat stress affects several processes during
plant growth and development, such as hypocotyl and petiole elongation 96, while elevated
ambient temperature has a positive effect on flowering 2,97 and a negative effect on stomata
formation 98. Several genes contribute to thermotolerance. Li and colleagues systematically
analysed the transcriptional regulatory network in Arabidopsis plants after exposure to Heat
Shock (HS) at 37°C using RNA sequencing (RNA-seq) 99. They determined that HEAT SHOCK
FACTOR A1 family proteins (HSFA1s), and the circadian clock proteins REVEILLE4 (RVE4) and
REVEILLE8 (RVE8), are among the primary transcription factors that mediate the first wave of
13
HS-induced gene expression – providing insight into how the circadian clock helps plants
adapt to high temperatures during the day. During HS, HSFA1s regulate transcriptional
responses leading to thermotolerance (Figure 3A-B). However, their activity is suppressed
under normal temperature environments through the action of HEAT SHOCK PROTEIN 70
(HSP70) and HSP90 (Figure 3A-B) 100–102. Although not considered HS, high temperatures
between ~29-36°C (supraoptimal) independently impact plant developmental responses. One
example of this is inhibition of seed germination at supraoptimal high temperatures
(thermoinhibition) 103. High temperatures during seed imbibition activate expression of
SOMNUS (SOM), which prevents seed germination by increasing ABA seed content and
reducing GA biosynthesis 104. Similarly, although warm temperatures accelerate flowering
(see below), supraoptimal temperatures delay it through upregulation of FLOWERING LOCUS
C, a MADS-box TF that represses flowering. This upregulation is due to higher protein stability
of the chromatin modifier JUMONJI 30 (JMJ30) at 29°C, which prevents the accumulation of
H3 lysine 27 di- and trimethylation (H3K27me2/3) at FLC 105. These joint mechanism of delay
of flowering and germination (thermoinhibition) by supraoptimal conditions may have
important implications to seed set and survival when germinating under adverse
environmental conditions.
The developmental response to warm temperatures, such as longer hypocotyls and petioles
and more rapid flowering (thermomorphogenesis, ~20-28°C), is a separate process to HS
(>37°C) and the supraoptimal high temperature response. PIF4, PIF5, and PIF7, discussed
above for their role in light signalling, play a vital role in the positive regulation of plant
thermomorphogenesis 106,107. Rapid induction of PIF4 expression has been observed to occur
during early evenings due to warm temperatures and it is negatively regulated by the evening
complex EARLY FLOWERING 3 (ELF3), ELF4, and LUX ARRHYTHMO (LUX) (Figure 3C) 108.
Another set of negative regulators of PIF4 are POWERDRESS (PWR) and its interactor HISTONE
DEACETYLASE 9 (HDA9), which control thermomorphogenesis through the induction of H3
deacetylation (Figure 3C) 109. On the other hand, SHORT HYPOCOTYL UNDER BLUE 1 (SHB1) is
recruited by the core components of the circadian clock CIRCADIAN CLOCK-ASSOCIATED 1
(CCA1) and LATE ELONGATED HYPOCOTYL (LHY) to positively regulate the expression of PIF4
(Figure 3C) 110. Further, the transcription factors TEOSINTE BRANCHED 1/CYCLOIDEA/PCF 5
14
(TCP5) and BRASSINAZOLE-RESISTANT 1 (BZR1) have been recently demonstrated to play a
role in the positive regulation of PIF4 in the thermomorphogenic response (Figure 3C) 111,112.
In addition, the UV-B receptor UVR8 and the light signalling TF HY5 have separately been
demonstrated to impair the thermomorphogenic response through negative regulation of
PIF4 expression (Figure 3C) 113,114. During hypocotyl thermomorphogenesis, COP1 is imported
into the nucleus where it reduces the negative regulation of HY5 on hypocotyl growth (Figure
3D). cop1 mutants have been shown to be defective in PIF4 expression and warmth-induced
hypocotyl elongation 114,115. Another key light-signaling component that plays a role in
thermomorphogenesis is DET1. Together with COP1, DET1 is essential for the transcriptional
regulation of PIF4 through HY5 (Figure 3D) 116. PIF4 then regulates hypocotyl elongation
through auxin biosynthesis genes (e.g. TAA1, CYP79B2 117 and YUC8 118) and auxin responsive
proteins (e.g. IAA19, IAA29 119). Auxin biosynthesis in response to PIF4 occurs primarily in the
epidermis of cotyledons and auxin acts as a mobile signal, travelling to the hypocotyl where
it induces elongation in combination with local signals 120,121.
HY5 expression can also be induced by cold stress where it plays a positive regulatory role in
the expression of the COLD REGULATED (COR) genes via the function of the Z-box and other
cis-acting elements in their promoters (Figure 3E) 122. The expression of HY5 under cold stress
is independent of the other major cold-stress pathway 122. This latter involves the three CBF
genes, CBF1, CBF2, and CBF3, and their transcriptional regulatory pathway (Figure 3F) 123,124.
Low temperatures bring on the swift induction of CBF gene expression and the consequential
activation of COR gene expression. Another transcription factor that plays a role in cold
acclimation is the bHLH transcription factor INDUCER OF CBF EXPRESSION 1 (ICE1) and its
homolog ICE2, with both of them playing a role in the response to deep freezing through a
CBF-dependent pathway in Arabidopsis thaliana plants (Figure 3F) 125,126. The role of ICE1 in
freezing tolerance is modulated through its phosphorylation by OPEN STOMATA 1 (OST1) 127.
OST1 is a SNF1-related protein kinase that positively regulates freezing tolerance in plants
through inhibition of the interaction between the E3 ubiquitin ligase HIGH EXPRESSION OF
OSMOTICALLY RESPONSIVE GENE1 (HOS1) and ICE1, leading to a more stable form of ICE1
and therefore a sustained freezing tolerance response 127,128. Furthermore, OST1 plays a role
in improving the protein stability of CBF proteins through the phosphorylation of BASIC
TRANSCRIPTION FACTOR 3 proteins (Figure 3F) 129.
15
Other factors also play a role in plant mechanistic responses to cold stress h. For instance,
cold stress has been found to activate several regulatory responses, such as the CYTOPLASMIC
RECEPTOR-LIKE KINASE 1 (CRPK1) phosphorylation of 14-3-3 proteins, which induces their
interaction with and stabilisation of CBFs 130. Phosphorylation of ICE1 by the MAP kinases
MPK3 and MPK6, as well as by BRASSINOSTEROID INSENSITIVE 2 (BIN2), is also induced by
cold stress, leading to negative regulation of CBF expression 131,132. Nonetheless, these
extensive investigations of cold responses so far fall short of providing a comprehensive
understanding of the full pathway from cold-sensing to response in plant cold and freezing
acclimation.
As well as cold stress and freezing, plants also sense low temperatures over long periods as a
seasonal signal, in a process termed vernalisation (Figure 3G). Vernalisation is a prevalent trait
of plants in temperate zones and it means that exposure to long periods of cold promotes the
induction of flowering 133. In Arabidopsis, the regulation of vernalisation occurs through the
action of the floral transcriptional repressor FLC which inhibits FT, a component of the
flowering-inducing factor florigen 134,135. FLC expression is repressed by long-term cold, and
this process needs the PHD protein VERNALIZATION INSENSITIVE3 (VIN3), which is
quantitatively upregulated during cold. VIN3 seems to be regulated at the level of
transcriptional initiation by three independent temperature inputs, a fast temperature
response (minutes-hours), a short-term response to warmth (hours-days) and a slow
response to cold (weeks) 136,78. The latter was recently found to be mediated by NTL8 protein
accumulation in long periods of cold 95, but the faster thermosensors remain unknown. FLC
shutdown promotes flowering thermomorphogenesis, driven by both FT and other flowering
regulating genes that are activated 137,138.
16
Figure 3. Temperature driven transcription initiation.
A, Heat stress halts the inhibitory activity of HSP70 and HSP90 on HSFA1s, leading to their
disassociation from HSP70 and HSP90 and subsequent activation. B, Following the activation
of HSFA1s they in turn regulate the transcriptional initiation of several HSR genes such as
HSFA2 that trigger thermotolerance. C, Warm temperatures induce the expression of PIF4 by
inhibiting the expression of several of its negative regulators such as the evening complex
(ELF3, ELF4, LUX), PWR/HAD9, UVR8 and HY5. Warm temperatures also lead to the positive
regulation of PIF4 expression under the influence of several positive regulators such as
CCA1/LHY/ SHB1, TCP5, and BZR1. D, Warmth causes both COP1 and DET1 to actively
attenuate HY5 stability leading to its degradation and the subsequent induction of expression
of PIF4. PIF controls auxin responsive proteins (e.g. IAA19) as well as auxin biosynthesis genes
17
(e.g. YUC8), indicated as ARP and ABG respectively in the schematic. E, Cold temperatures
induce the expression of HY5 and increase its stabilisation through nuclear depletion of COP1
and in turn initiate cold stress responses. F, Under cold and freezing stress, ICE1 is
phosphorylated and stabilised by the protein kinase OST1 which interrupts ICE1
ubiquitination and degradation by the E3 ligase HOS1. Stabilisation of ICE1 leads to the
initiation of the transcription of several COR genes leading to the triggering of cold acclimation
and freezing tolerance. G, During vernalisation, perception of winter cold temperatures
(Phase I) triggers the quantitative inactivation of FLC transcript (green solid line). In the
absence of the cold signal during spring, epigenetic memory (Phase II) maintains the FLC at
low levels. FLC silent state correlates with the accumulation of the H3K27me3 repressive mark
at FLC chromatin. H, Transcriptional memory of Heat Stress (HSt) can also be divided into
distinct phases. Perception of high temperatures induces activation of HSt memory genes
(Phase I). Upon removal of the heat signal (Phase II or primed state), HSt memory genes can
exhibit sustained (green solid line) or baseline (green dotted line) expression levels, with their
chromatins coated by the H3K4me2/3 active marks. HSt memory genes show higher or faster
activation following recurrent heat stress (Phase III) conferring on the plant the ability to
prevent damaging effects.
3. DIVERGENT EFFECTS OF LIGHT AND TEMPERATURE ON PLANT
TRANSCRIPTION
Light sensing is translated into both cytoplasmic and chloroplast retrograde signalling
pathways that converge in specific TFs to regulate transcriptional initiation. Temperature-
induced transcriptional regulation diverges from light because it will not only influence the
set of genes being turned ON or OFF by specific TFs, but may also directly affect the physical
properties of nascent RNA transcript processing and RNAPII kinetics. In the following sections,
we summarise the direct and indirect effects of temperature and light, respectively, on the
regulation of co-transcriptional processes in plants.
18
3.1. DIRECT EFFECT OF TEMPERATURE ON CO-TRANSCRIPTIONAL PROCESSES
It has been recently proposed that temperature sensing in plants is distributed across
regulatory networks, with multiple temperature inputs combined to control each process 78.
Such a temperature sensing system could be controlling the abundance of the TFs described
previously, but it could also be directly affecting mechanisms relating to transcription,
following transcriptional initiation. Co-transcriptional processes such as elongation, RNAPII
stalling at gene borders, splicing, termination and polyadenylation may also be sensitive to
temperature (Figure 1B-D). In warm-blooded mammals, it has been proposed that cooling
stabilises secondary structures of pre-mRNAs affecting splice site selection 139. In plants, given
their sessile nature, physical perturbations on macromolecules caused by temperature
variation are likely to be even more dramatic.
Recent studies have started to elucidate distinct features of nascent transcription in plants
140–144 with particular attention given to how cooling influences co-transcriptional processes
145. A detailed time series during cold acclimation in Arabidopsis revealed dynamic changes in
expression of several genes, including induction of previously characterised cold-inducible
genes, as well as massive changes in alternative splicing (AS) patterns 146. Over a quarter of
genes whose expression changes significantly in the cold also undergo AS. Among the
differentially spliced genes identified, some had previous evidence of involvement in cold
responses, such as REGULATOR OF CBF EXPRESSION 1 (RCF1), PIF7 and PHYB. In addition to
protein coding genes, hundreds of long non-coding RNAs (lncRNAs) are differentially
expressed and alternatively spliced in response to cold 147. Variation in gene splicing patterns
occurs rapidly upon cold exposure and can be sensitive to temperature reductions as small as
2°C 146. AS makes a major contribution to changes in the transcriptome, amplifying the ability
of temperate plants to grow in a wide range of fluctuating temperatures, as influencing the
spliceform generated from each locus increases the potential transcriptomic variation that a
signal cascade can induce. Temperature-induced AS could be caused by either a direct effect
on the splicing components and the secondary structure of the nascent RNA, or the result of
the variation of RNAPII kinetics as temperature decreases. Indeed, the application of a NET-
seq approach in Arabidopsis (plaNET-seq) has shown transient molecular adaptations of
RNAPII transcription in response to cold 145,148. RNAPII kinetics are modulated as temperature
decreases leading to changes in transcriptional elongation and termination. Interestingly, the
19
dynamics of the splicing reaction are initially affected during early stages of cold acclimation
but later recover to normal levels, reinforcing the influence of AS in rapid responses to cold.
Elevated ambient temperature and heat stress can also impact co-transcriptional processes
in plants. Temperature-induced differential accumulation of two FLOWERING LOCUS M (FLM)
splice variants, FLM and FLM, regulates Arabidopsis floral transition 149. Whereas low
ambient temperature favours accumulation of FLM that actively represses flowering, rising
temperature increases the FLM/FLM ratio to release floral repression. In addition to
splicing, FLM levels are also reduced by the Nonsense-Mediated mRNA Decay (NMD) pathway
under elevated temperatures resulting in floral induction 150. Heat stress also has a strong
effect on mRNA splicing. The U5-snRNP-interacting protein STABILIZED1 (STA1) is a heat
inducible gene involved in the splicing of heat shock factors (HSF) and HSP transcripts during
high temperature stress 151. Interestingly, STA1 had originally been found to regulate the
splicing of cold responsive genes such as COR15A under low temperature stress 152.
Widely present in mammals and metazoans, the process of RNAPII stalling over gene
boundaries was recently demonstrated in plants 140,143. Engaged RNAPII initially transcribes
20–60 nucleotides before undergoing promoter-proximal (5’ end) pausing, a regulatory
checkpoint for execution of transcription programmes 153. In Arabidopsis, promoter-proximal
stalling of RNAPII transiently increases at early stages of cold acclimation to adjust
transcription to low temperatures 145. In addition to promoter-proximal stalling, RNAPII stalls
near 3’ ends of Arabidopsis genes 141–143. Cold exposure significantly decreases the 3’ end peak
of RNAPII observed when the polymerase is stalled downstream of the Polyadenylation Site
(PAS), suggesting a major change in transcription dynamics associated with termination in
response to low temperatures 145.
3.2. PHOTORECEPTOR-MEDIATED EFFECTS ON CO-TRANSCRIPTIONAL RESPONSES
Light also controls co-transcriptional processes such as choice of Transcription Start Site (TSS),
pre-mRNA- and alternative- splicing of large numbers of genes, with mechanisms distinct
from those controlling transcriptional responses 148,154–163. In the case of light-induced
alternative TSS use, this leads to changes in protein fate. Ushijima and colleagues found that
red-light activated phyB alters TSS usage for over 2000 loci, enriched in plastid-targeted
proteins, and the resulting changes in N-terminal signal sequence leads to changes in
20
subcellular protein localisation for nearly a fifth of these genes 163. In contrast, Kurihara et al.
investigated blue light, finding that a small (~200) subset of target genes have TS sites both
upstream and downstream of short open reading frames in the 5’UTR of the main coding
sequence 155. These upstream open reading frames can trigger transcript degradation through
the NMD pathway, or interfere with translation itself, both routes leading to reduced protein
output 164. Blue light promotes use of the downstream, protein-producing TSS in most cases,
a response partially mediated via HY5, which has binding sites within many of the target
promoters 155. Like the red-light response, the blue light target set is enriched in light
responsive genes, and both responses modulate the photorespiration pathway to cope with
effects of fluctuating light on the photosynthetic machinery 155,163.
Like temperature, light also induces alternative splicing, in the majority of cases promoting
production of protein-encoding splice variants over those with NMD features 165. At least two
sets of photoreceptors are known to mediate this response. One reacts to white light intensity
via chloroplast retrograde signalling in response to Photosystem II function 158,165,166. The
other route requires red-light sensitive phytochrome action and is conserved across the land
plants 159,161,162,165,167–169. These routes are independent but not mutually exclusive, and
converge on serine/arginine-rich (SR) splicing factors such as RS31 160,161.
Phytochrome-dependent AS is critical for phy-mediated photomorphogenesis and regulates
several transcription factors, such as PIF3, PIF6 and ELF3, and negative regulators, such as
SPA3, required for light-signalling itself 159,161,162,169,170. The mechanism of phytochrome-
dependent AS appears to be through direct interaction of phyB with the pre-mRNA splicing
factors REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND1 (RRC1) and SPLICING
FACTOR FOR PHYTOCHROME SIGNALING (SFPS) 162,167,169. In Arabidopsis, the interaction
between RRC1 and phyB is light-induced but independent of the Pr/Pfr conformation of phyB
162, whereas in the moss Physcomitrella patens, interaction between PpPhy4, a phyB
homologue, and the splicing regulator PphnRNP-F1 is red-light specific, and induces
interaction of PphnRNP-F1 with other spliceosome components 171,172. In Arabidopsis, RRC1
is itself alternatively spliced in an SFPS-dependent response to light, providing a positive
feedback loop 162,165,167.
At least part of the light-driven AS response seems to occur due to enhanced RNAPII
elongation in response to light 166. It is unlikely that light will directly modulate the physical
properties of RNAPII and RNA transcripts as has been suggested for temperature 145. Instead,
21
while the expression of the transcription elongation factor TFIIS itself is not affected,
members of the plant POLYMERASE ASSOCIATED FACTOR COMPLEX (PAF1-C), including
EARLY FLOWERING7, are transcriptionally upregulated in response to light and may provide
part of the mechanism 166. More directly, genetic evidence links stress-induced singlet oxygen
in the chloroplast to the activity of TOPOISOMERASE VI, which binds a subset of high-light
induced target promoters directly and may also enhance elongation 33. Recent work has
demonstrated a specific mechanism for integration of light into circadian-clock regulated
transcriptional activation via the NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED (LNK)
proteins 173. LNKs are transcriptionally upregulated in response to light, probably via
phytochrome signalling 174 and recruit RNPII and the transcript elongation FACT complex to
their targets via interaction with the MYB TF RVE8 173. Interestingly, RVE8 is also involved in
temperature responses 99.
Questions remain, however, on which responses are direct and which due to secondary
signalling 156. Many of the light-responsive AS genes are splicing factors themselves, leading
to a secondary cascade of AS throughout the plant 160–162. The presence of the AS response in
non-irradiated, chloroplast-lacking roots indicates the role of a secondary, non-cell-
autonomous system 158, possibly mediated via sugar signalling 165. As a result light, like
temperature, can affect genome-wide co-transcriptional processes at the whole plant level,
via secondary signalling.
In conclusion, both light and temperature generate genome-wide cascades of co-
transcriptional effects. However, while in the case of light these are generally triggered
through distinct receptor pathways and subsequent upregulation of the transcriptional
machinery, temperature can modulate transcription kinetics directly.
3.3 INDUCTION OF LONG NON-CODING TRANSCRIPTS
A common phenomenon observed in plant responses to light and temperature is the
induction of lncRNAs. During long cold periods, plants undergo massive transcriptional
reprogramming, which also results in the activation of lncRNAs. The FLC locus has provided a
highly informative system for studying the effects of these transcripts. COOLAIR lncRNAs,
antisense to FLC locus, significantly increases in expression levels in the first couple of weeks
of winter temperature 175,176. Transcription from the antisense strand may inhibit RNAPII firing
22
from the FLC sense strand, as suggested by the mutually exclusive expression of COOLAIR and
FLC nascent transcript at single loci resolution 177. Although the precise mechanism by which
COOLAIR suppresses nascent FLC expression during cold remains unknown, modulation of
chromatin dynamics is likely implicated in this process. Arabidopsis transgenic lines with
reduced COOLAIR function fail to remove the H3K36me3 mark at the FLC locus, resulting in
less efficient reduction of FLC nascent transcript during cold 175. This observation suggests
that cold-induced non-coding transcripts at FLC are required to set the chromatin landscape
for transcriptional inactivation.
Another cold-induced lncRNA also represses FLC via modulation of local chromatin
architecture. Expression of the sense lncRNA COLDWRAP from the sense FLC inactive
promoter induces the formation of an intragenic gene loop within the FLC locus to perpetuate
gene inactivation 178. Finally, the intronic sense lncRNA COLDAIR mediates PHD-PRC2 (PLANT
HOMEODOMAIN- POLYCOMB REPRESSIVE COMPLEX 2) recruitment to FLC for stable
epigenetic silencing 179. Another vernalisation-linked lncRNA, that does not map to the FLC
gene, is the MADS AFFECTING FLOWERING 4 (MAF4) antisense (MAS) transcript 180. MAS is
transcribed during cold exposure 180 mimicking the expression pattern of MAF4 181. Induction
of MAS seems to play a crucial role in the recruitment of COMPASS-like complexes to MAF4
chromatin to activate its expression 180. In all cases, it remains to be determined what pioneer
TFs trigger transcription of all these cold-induced lncRNAs.
Temperature-induced non-coding transcription has been shown to affect transcription
termination. Cold-induced transcription of the Arabidopsis CBF locus triggers expression of a
cascade of antisense transcripts that fine-tunes the level of CBF1 mRNA 182. The lncRNA
SVALKA, located downstream of the CBF1 gene, is transcribed from the antisense strand.
SVALKA transcription terminates downstream of the CBF1 locus in plants growing under warm
temperatures. During cold acclimation, however, RNAPII read-through transcription of
SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1.
The SVALKA-asCBF1 system limits the production of maximal CBF1 mRNA levels by a RNAPII
collision mechanism in the 3′-end of CBF1 182. Thus, the interplay of two lncRNAs tightly
regulating CBF1 mRNA levels allows plants to appropriately acclimate to low temperatures.
23
Increasing evidence shows that non-coding transcription also leads to the formation of R-
loops in the plant genome. R-loops are created by the invasion of the DNA duplex by
complementary RNA molecules, generating an RNA-DNA helix and leaving a single-stranded
section of complementary DNA. At the single gene scale, R-loops appear to be important for
transcriptional regulation 183–186. R-loop stabilisation at the promoter of COOLAIR is required
for correct expression of both COOLAIR and FLC 187. Invasion of the lncRNA APOLO (AUXIN
REGULATED PROMOTER LOOP) into a number of genomic loci, including auxin responsive
genes, results in R-loop formation and subsequent displacement of Polycomb repressive
activity leading to gene activation 188. However, construction of a genome-wide R-loop atlas
by the Sun lab revealed that R-loop presence does not strongly correlate with mRNA
transcript abundance 189. Indeed, genome wide R-loop patterns seem to be largely conserved
through many environmental perturbations, although developmental phase changes such as
germination and flowering have more noticeable effects 189. Exposure to long term heat stress
results in a slight increase in antisense R-loops localised to the TSS. A subset of these show
correlation of expression with the expression with known R-loop regulators during this
process, hinting at a regulatory role. However RNAPIII-transcribed genes, such as small
nucleolar RNAs and tRNAs, are consistently associated with higher R-loop levels in germinated
seedlings than germinating or dark-grown seedlings, raising the possibility that R-loop
dynamics may be particularly important for light regulation of RNAPIII transcription 189.
Further work on individual gene dynamics and R-loop regulators will shed more light on the
mechanistic basis of these responses and their biological role.
Similar genome-wide studies of lncRNAs in response to light have focused on natural
antisense transcripts (NATs) in de-etiolating seedlings 190. A majority of light-induced
‘concordant’ NAT (those changing expression in the same direction as the coding transcript)
are principally expressed in cotyledons and include members of the light-sensing pathway
such as SPA1 and HYH. Light also induces a number of long intergenic non-coding RNAs of
unknown functional significance 165. Further detailed work is required to functionally
characterise the mechanism and roles of these light-induced lncRNAs.
24
3.4 BOTH LIGHT AND TEMPERATURE IMPACT PLANT CHROMATIN DYNAMICS
Plants monitor temperature changes both diurnally and seasonally. Temperature may
physically alter the interaction of DNA with nucleosomes and thus have a direct effect on
chromatin compaction 191. Not surprisingly, plant genes may display unique chromatin
signatures in response to temperature cues 192. As mentioned above, elevated temperatures
trigger a universal response which involves the rapid upregulation of heat shock proteins
(HSPs) 193. Heat stress, which for Arabidopsis usually means exposing plants to temperatures
above 36°C, induces substantial changes to plant nuclear architecture, including decrease of
heterochromatin compaction 194 and decondensation of chromocentres 195. DNase-seq
studies revealed that the degree of chromatin accessibility changes dynamically upon heating
196. The most highly accessible genes following heat shock encode heat shock proteins and
several heat-stress-related TFs, which correlates with their rapid activation. Similarly, heat
shock results in the reduction of nucleosome density, mediated by HEAT INTOLERANT 4 (HIT4)
197.
Moving from dark to light also results in major changes in nuclear organisation such as
decondensation of chromocentres and decompaction of heterochromatin, especially during
photomorphogenesis 192,198–201. As well as the large-scale transcriptional reprogramming
associated with the developmental aspects of photomorphogenesis, high light is a cellular
stress, and UV irradiation causes DNA damage. Responses to all these aspects are united by
the multifunctional roles of DET1 60. As well as its role in stabilisation of PIF proteins 56, DET1
also has roles in the repair of UV-induced DNA damage through the global genome repair
pathway 59. In addition, DET1 binds directly to non-acetylated tails of histone H2B 202 and is
required for the global increase in H2B ubiquitination that is induced by light 203, via DET1-
mediated degradation of a deubiquitination module of the SAGA complex 204. Correct H2Bub
is required for light-induced transcription change and seems particularly important for genes
that respond especially rapidly 203.
Besides heat shock, more moderate variation in ambient temperature also impacts plant
chromatin and transcription. In fact, temperature changes as little as 1°C may lead to gene
reprogramming, and can also affect crop yield 205. As part of the thermomorphogenic
response, in Arabidopsis thaliana nucleosomes containing the histone variant H2A.Z are
25
evicted from the chromatin of thermo-responsive genes when temperature rises from 22°C
to 27°C 92 resulting in transcriptional change dependent on the locus. H2A.Z nucleosomes may
act to enhance the transcriptional dynamic range by keeping genes transcriptionally
repressed under non-inductive conditions via restriction of promoter and gene accessibility.
Histone deacetylation by HDA9 also facilitates H2A.Z nucleosome eviction from the promoter
of the thermo-responsive gene YUC8 under warmer temperature 206 resulting in
transcriptional activation. This process, likely occurring downstream of HSFs, extends our
view of histone deacetylation, which is generally associated with transcriptional repression.
In addition, histone H3 lysine 36 methylation (H3K36me3) affects temperature-induced
alternative splicing, potentially by facilitating the recruitment of splicing factors to the
chromatin during transcription 207. Whether H3K36me3 dynamics could be acting as a
thermosensor needs further validation. More generally, the ability of any chromatin structure
to directly sense a temperature change to control thermal responses remains an open
question 79.
Increases in histone acetylation appear to be a general part of light-induced chromatin
changes that are associated with the transcriptional upregulation of many genes, including
HY5 and HYH 208. Indeed, addition and removal of acetylation at HY5 and PIF target genes may
form part of the antagonistic actions of these light regulators on transcription. For example,
Peng et al. find that PIF recruits HISTONE ACETYL TRANSFERASEs (HATs) to regulate shade
response 209, while Yang et al. find HY5 recruits HDA9 to repress target genes involved in
autophagy in the dark 210. HISTONE DEACETYLASE 15 (HDA15) is also recruited to targets by
both PIF1 and PIF3 to mediate repression by deacetylation of target genes 211,212.
PIF1 additionally recruits another form of histone modifier to its targets: the SWI/SNF
complex member BRAHMA (BRM) 213. BRM acts with PIF1 to reduce H3K4 methylation and
expression of chlorophyll biosynthesis genes in the dark, preventing photobleaching during
subsequent irradiation. PIF1 itself is under chromatin regulation, with normal PIF1 expression
requiring the H3K36 methylase SDG8 214.
Downstream of light-regulated transcription itself, several chromatin modifiers have been
characterised as necessary for light response. Among the chromatin modifiers themselves
transcriptionally regulated in response to light are several Jumonji-domain proteins. JMJ20
26
and JMJ22 are upregulated in response to red light, and enhance seed germination by
demethylating histone H4 arginine residues and thereby derepressing gibberellin synthesis
loci 215. The H3K27me3 demethylase JMJ30/JMJD5, which acts at FLC in response to high
temperatures, is also alternatively spliced in response to light, although the functional
significance of this is unknown 160. JMJ30 is involved in temperature compensation of the
circadian clock 216, potentially providing another route for light and temperature integration
at the chromatin level. In addition, the ATP-dependent chromatin remodelling factor PICKLE
(PKL) acts downstream of both light and temperature signalling to promote Arabidopsis
growth 217,218 thus providing further integration of light and temperature signals through
chromatin regulation.
3.5 LONG TERM MEMORY OF ENVIRONMENTAL STIMULI PERCEPTION
So far, we have discussed how perception of specific cues results in transient transcriptional
regulation. However, many transcriptional reprogramming events, as is the case for
acquisition of stress tolerance and developmental switches, should persist for prolonged
periods of time even in the absence of the triggering signal 219,220. In those cases, two distinct
phases can be distinguished in the response (Figure 3G-H): initial and rapid up- and down-
regulation of genes induced by perception and integration of a specific cue from the
surroundings (Phase I); and perpetuation of the acquired ACTIVE or INACTIVE potential of
those genes for extended periods of time by epigenetic mechanisms, in the absence of the
inductive cue (Phase II).
The best characterised example of such an epigenetic process is the silencing of the gene FLC
in vernalisation, and the memory of the silencing following winter (Figure 3G). The FLC gene
is highly expressed in vernalisation-requiring accessions of Arabidopsis, until the plants
experience prolonged cold 221. Increasing weeks of cold temperature trigger the inactivation
of FLC transcription (Phase I) and this is accompanied by the build-up of the epigenetic
silencing apparatus at FLC chromatin. Subsequently, Phase II secures the maintenance of the
FLC silent state once the cold signal has disappeared (Figure 3G).
During Phase I, exposure to cold temperatures induces epigenetic silencing of FLC by the
action of lncRNAs (COOLAIR, COLDAIR, COLDWRAP, as discussed above), by the sequence-
specific transcriptional repressors (VAL1 and VAL2 proteins, 222,223) and by the PRC2 combined
27
with Plant Homeodomain (PHD) proteins (PHD-PRC2 complex; 224,225). PHD-PRC2 assembles
at FLC chromatin during cold and deposits the H3K27me3 histone repressive mark at
individual FLC loci 226–230 while histone demethylases remove the chromatin active marks
(H3K36me3 and H3K4me3) that were present in those nucleosomes 231.
After the cold signal is gone, the individually silenced FLC copies remain transcriptionally
inactive allowing the plants to remember the cold period and quantify its duration (Phase II,
Figure 3G). Upon return to warm temperatures, H3K27me3 spreads from the nucleation
region to cover the FLC locus (Figure 3G)225,226,228–230.
Cold-sensing is not just a signature for floral induction. Plants are able to remember cold
stress to enhance survival when they are exposed to low temperatures a second time 232,233.
Before cold stress, H3K27me3 coats the genomic region of a subset of early-cold inducible
genes required to trigger cold acclimation 234–236. Therefore, PRC2-mediated repression likely
prevents activation of these loci under non-stress conditions 236. However, H3K27me3 does
not seem to control short-term cold-stress memory 236 as it does for the long-term
maintenance of FLC silencing during vernalisation. Future work will reveal the chromatin
components underlying cold stress transcriptional memory.
A well-documented example of stress memory is thermotolerance, where perception of
moderate HS allows plants to subsequently withstand high temperatures that would
otherwise be lethal 237. A number of genes, including HSP22.0 and ASCORBATE PEROXIDASE
2 (APX2), are initially activated during the priming HS and their expression levels are either
sustained or downregulated to basal levels in the absence of the inductive cue 238 (Figure 3H).
Either way, they show an increased response after a recurring HS days after the primary HS,
consistent with the definition of transcriptional memory (Figure 3H)239. HS transcriptional
memory at the memory-related loci HSP22.0 and APX2 depends on the sustained
accumulation of H3K4me3 and H3K4me2 239. Both HS transcriptional memory and the
sustained H3K4me3 and H3K4me2 depend on the HEAT SHOCK TRANSCRIPTION FACTOR A2
(HSFA2) 239. In addition, the Arabidopsis homologue of the metazoan Strawberry Notch
protein FORGETTER 1 (FGT1) is required for HS memory. FGT1 associates with the promoters
of HS memory-related genes to ensure proper nucleosome remodelling during the acquisition
of thermotolerance 240. By analogy to vernalisation, plant HS memory can also be divided into
28
two phases (Figure 3H) corresponding to “perception” (Phase I) and “memory” or “primed
state” (Phase II). Additionally, stress memory exhibits a unique Phase III that correlates with
the rapid or altered transcriptional responses to the recurrence of the triggering signal (Figure
3H).
Another example of transcriptional stress memory occurs during recurring dehydration
stresses 241. In this case, not only does H3K4me3 act as a persistent epigenetic mark, but in
addition stalling of the phosphorylated serine 5 form of RNAPlI (Ser5P) is associated with
transcriptional memory 241. Interestingly, light signalling via phytochromes is required for
transcriptional memory of the salt- and dehydration-stress inducible gene Δ1-PYRROLINE-5-
CARBOXYLATE SYNTHASE 1 (P5CS1, 242). HY5 and HYH are not required for initial upregulation
of P5CS1, but HY5 binding to the promoter is necessary for maintenance of H3K4me3 levels
at the locus for enhanced response to repeated stimuli 242.
Undoubtedly, chromatin dynamics play a key role in plant adaption to light fluctuations
192,200,243. However, the existence of mechanisms of transcriptional stress memory in the field
of light stress responses remains an open question. Exposure to high light results in priming,
or photoacclimation, as well as in the induction of a systemic acquired response that renders
non-exposed leaf tissues less susceptible to recurrent exposure to light stress 244–247.
However, efforts to try to link epigenetic modifications, e.g. DNA methylation, with the
acquisition of a “primed state” following excess light stress have not been successful 247,248.
Follow up studies will be necessary to reveal what are the chromatin components taking part
in these mechanisms that prime plants to rapidly respond to harmful irradiation.
7. CONCLUDING REMARKS
Light and temperature are the two most important environmental signals to determine
seasonal progression and correct timing of development for most plants. At the same time,
they are linked to the plants ability to produce energy, capture CO2 and survive other stresses
in direct ways, as well as being potential stressors themselves. Therefore, it is not surprising
that plants have a complex way of responding to each of these signals separately, and that
they also become integrated in many responses. The pathways of environmental signalling
have multiple stages, starting with signal perception by “sensors” (Phase I), followed by
downstream transcriptional cascades and in some cases long-term memory of the signal
29
(Phase II/III). The presence and duration of this memory will depend on the nature of the
signal and the desired response. For example, in stress response, the experience of a stress
now is likely to indicate that the same or a related stress will occur again in the near future.
However, the opposite is true in more long-term signalling that determines seasonal
progression such as vernalisation, which tells the plant that winter has passed and is unlikely
to occur again for a long time.
In the perception of environmental signals, it is very hard to distinguish direct, sensor-
mediated responses and indirect, downstream transcriptional cascades, and so the search to
identify the primary sensors has been a difficult one. For light sensors, which have more
distinctive properties, many have been known for a long time. Temperature instead has more
direct effects in biochemistry and so most processes can contribute to its perception, making
temperature sensing a question of integration of (often subtle) inputs from multiple
“thermosensors”. Thus, plant thermosensors, unlike light sensors, remain largely unexplored.
Furthermore, though the mechanism of its significance is still unknown for most cases, the
fluctuating nature of the temperature signal has a strong effect on its perception 136,249,250.
This highlights the pressing need for further knowledge on the subject, considering the
important role of thermosensing in plant growth, development and temperature stress
acclimation. Under a scenario of global temperature increase, in combination with an
increase in extreme events, knowledge on how to modulate plant thermosensing
mechanisms would provide great advantages for crop breeding and growth.
Regarding transcriptional regulation, light and temperature have similar yet divergent effects.
Following perception, the underlying signalling pathways converge in the function of
numerous TFs, some of which are common to both cues. In addition, temperature affects the
photosensitive reactions of several of the known light receptors, thus signalling is integrated
from the start. The application of novel transcriptomic technologies has now allowed to shift
the focus from TFs to the analysis of effects on splicing, RNAPII elongation rate and stalling in
plants. In the case of light, thus far these effects seem to be mediated through TF control of
the components of the transcriptional and splicing complexes. However, this has not yet been
found in analyses of temperature effects. These initial key findings will pave the way for future
studies to determine whether the components of the transcriptional machinery (RNAPII,
spliceosome, nascent RNA) are themselves thermosensors. Given the highly structured
30
nature of RNA molecules, the possibility remains that nascent RNAs may adopt dynamic
conformational changes directly modulating co-transcriptional processes. Despite advances
in recent years, research on RNA in vivo structures in plants is still in its early days. Efforts in
this direction should focus on investigating perturbations to RNA molecules in plants growing
in natural habitats, to ensure their biological relevance.
Both light and temperature signalling converge in modulation of chromatin states. These
dynamic changes in chromatin conformation become themselves part of the signalling
process by controlling expression of numerous genes both short and long term. Chromatin
changes that follow light perception are very likely a consequence of the action of
photoreceptor-induced TFs. Conversely, temperature may directly perturb physical
conformations of chromatin, but conclusive in vivo examples of such processes are still
missing. Work is required to define to what extent nuclear chromatin is responsive to
temperature variation. In parallel, possible thermal effects on the kinetics of the catalytic
activities of chromatin “readers” and “writers” should also be evaluated.
In this context, precise, quantitative analysis of the responses to temperature and light levels
are required to dissect the contribution of each mechanism to the overall response.
Moreover, the sheer complexity of these interacting, simultaneous processes will likely
require mathematical and computational approaches to elucidate non-intuitive results. Such
approaches, very informative in dissecting the mechanism of photomorphogenesis 251, have
already begun to bear fruit in the identification of the elusive plant thermosensors.
ACKNOWLEDGEMENTS
We are grateful to Paloma Mas and Jordi Moreno-Romero for critical comments on the
manuscript. We apologise for not citing all the relevant primary research articles and reviews
due to space limitation. J. H. and RLAK were supported by Biotechnology and Biological
Sciences Research Council grants; BB/P020380/1 (R.L.A.K), Brassica rapeseed and vegetable
optimisation strategic Lola (BB/P003095/1) (J.H.); and the “Genes in the environment”
Institute Strategic Programme (BB/P013511/1) (J.H. and R.L.A.K). M.J. and J.I.Q. were
31
supported by the Severo Ochoa Excellence Programme. J.I.Q. is grateful to the support of a
fellowship from ”la Caixa” Foundation (ID 100010434). The fellowship code is
LCF/BQ/PI19/11690003”.
DISCLOSURE OF POTENTIAL CONFLICTS OF INTEREST
The authors declare no conflicts of interest.
REFERENCES
1. Blázquez, M. A., Ahn, J. H. & Weigel, D. A thermosensory pathway controlling flowering
time in Arabidopsis thaliana. Nat. Genet. 33, 168–171 (2003).
2. Balasubramanian, S., Sureshkumar, S., Lempe, J. & Weigel, D. Potent induction of
Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genet 2, e106
(2006).
3. Andrés, F. & Coupland, G. The genetic basis of flowering responses to seasonal cues.
Nature Reviews Genetics 13, 627–639 (2012).
4. Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–
4060 (2004).
5. de Santa, F. et al. A large fraction of extragenic RNA Pol II transcription sites overlap
enhancers. PLoS Biol. 8, (2010).
6. Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large
non-coding RNAs in mammals. Nature 458, 223–227 (2009).
7. Wissink, E. M., Vihervaara, A., Tippens, N. D. & Lis, J. T. Nascent RNA analyses: tracking
transcription and its regulation. Nature Reviews Genetics 20, 705–723 (2019).
8. Brahma, S. & Henikoff, S. Epigenome Regulation by Dynamic Nucleosome Unwrapping.
Trends in Biochemical Sciences 45, 13–26 (2020).
9. Fiszbein, A., Godoy Herz, M. A., Gomez Acuña, L. I. & Kornblihtt, A. R. Interplay Between
Chromatin and Splicing. in Chromatin Regulation and Dynamics 191–209 (Elsevier Inc.,
2017). doi:10.1016/B978-0-12-803395-1.00008-3
10. Berry, S., Dean, C. & Howard, M. Slow Chromatin Dynamics Allow Polycomb Target
Genes to Filter Fluctuations in Transcription Factor Activity. Cell Syst. (2017).
32
doi:10.1016/j.cels.2017.02.013
11. Steffen, P. A. & Ringrose, L. What are memories made of? How Polycomb and Trithorax
proteins mediate epigenetic memory. Nat Rev Mol Cell Biol 15, 340–356 (2014).
12. Yu, J.-R., Lee, C.-H., Oksuz, O., Stafford, J. M. & Reinberg, D. PRC2 is high maintenance.
Genes Dev. (2019). doi:10.1101/gad.325050.119
13. Reinberg, D. & Vales, L. D. Chromatin domains rich in inheritance. Science (80-. ). 361,
(2018).
14. Stewart-Morgan, K. R., Petryk, N. & Groth, A. Chromatin replication and epigenetic cell
memory. Nat. Cell Biol. 22, (2020).
15. Galvão, V. C. & Fankhauser, C. Sensing the light environment in plants: Photoreceptors
and early signaling steps. Current Opinion in Neurobiology 34, 46–53 (2015).
16. Franklin, K. A. & Quail, P. H. Phytochrome functions in Arabidopsis development. J. Exp.
Bot. 61, 11–24 (2010).
17. Legris, M., Ince, Y. Ç. & Fankhauser, C. Molecular mechanisms underlying
phytochrome-controlled morphogenesis in plants. Nature Communications 10, 1–15
(2019).
18. Jung, J.-H. et al. Phytochromes function as thermosensors in Arabidopsis. Science (80-.
). 354, 886–889 (2016).
19. Legris, M. et al. Phytochrome B integrates light and temperature signals in Arabidopsis.
Science (80-. ). 354, 897–900 (2016).
20. Wang, Q. & Lin, C. Mechanisms of Cryptochrome-Mediated Photoresponses in Plants.
Annu. Rev. Plant Biol. 71, (2020).
21. Yang, Z. et al. Cryptochromes Orchestrate Transcription Regulation of Diverse Blue
Light Responses in Plants. Photochem. Photobiol. 93, 112–127 (2017).
22. Vanhaelewyn, L. et al. REPRESSOR OF ULTRAVIOLET-B PHOTOMORPHOGENESIS
function allows efficient phototropin mediated ultraviolet-B phototropism in etiolated
seedlings. Plant Sci. 252, 215–221 (2016).
23. Christie, J. M., Blackwood, L., Petersen, J. & Sullivan, S. Plant Flavoprotein
Photoreceptors. Plant Cell Physiol. 56, 401–413 (2015).
24. Somers, D. E., Schultz, T. F., Milnamow, M. & Kay, S. A. ZEITLUPE encodes a novel clock-
associated PAS protein from Arabidopsis. Cell 101, 319–329 (2000).
25. Imaizumi, T., Tran, H. G., Swartz, T. E., Briggs, W. R. & Kay, S. A. FKF1 is essential for
33
photoperiodic-specific light signalling in Arabidopsis. Nature 426, 302–306 (2003).
26. Kim, W. Y. et al. ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue
light. Nature 449, 356–360 (2007).
27. Heijde, M. & Ulm, R. UV-B photoreceptor-mediated signalling in plants. Trends in Plant
Science 17, 230–237 (2012).
28. Favory, J.-J. et al. Interaction of COP1 and UVR8 regulates UV-B-induced
photomorphogenesis and stress acclimation in Arabidopsis. EMBO J. 28, 591–601
(2009).
29. Rizzini, L. et al. Perception of UV-B by the arabidopsis UVR8 protein. Science (80-. ).
332, 103–106 (2011).
30. Kaiserli, E. & Jenkins, G. I. UV-B promotes rapid nuclear translocation of the Arabidopsis
UV-B-specific signaling component UVR8 and activates its function in the nucleus. Plant
Cell 19, 2662–2673 (2007).
31. Di Wu et al. Structural basis of ultraviolet-B perception by UVR8. Nature 484, 214–219
(2012).
32. Keun, P. L., Kim, C., Landgraf, F. & Apel, K. EXECUTER1- and EXECUTER2-dependent
transfer of stress-related signals from the plastid to the nucleus of Arabidopsis thaliana.
Proc. Natl. Acad. Sci. U. S. A. 104, 10270–10275 (2007).
33. Šimková, K. et al. Integration of stress-related and reactive oxygen species-mediated
signals by Topoisomerase VI in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 109,
16360–16365 (2012).
34. Strand, Å., Asami, T., Alonso, J., Ecker, J. R. & Chory, J. Chloroplast to nucleus
communication triggered by accumulation of Mg-protoporphyrinix. Nature 421, 79–83
(2003).
35. Koussevitzky, S. et al. Multiple Signals from Damaged Chloroplasts Converge on a
Common Pathway to Regulate Nuclear Gene Expression. Science (80-. ). (2007).
36. Sun, X. et al. A chloroplast envelope-bound PHD transcription factor mediates
chloroplast signals to the nucleus. Nat. Commun. 2, 1–10 (2011).
37. de Souza, A., Wang, J.-Z. & Dehesh, K. Retrograde Signals: Integrators of Interorganellar
Communication and Orchestrators of Plant Development. Annu. Rev. Plant Biol. 68, 85–
108 (2017).
38. Zhao, X., Huang, J. & Chory, J. Unraveling the Linkage between Retrograde Signaling
34
and RNA Metabolism in Plants. Trends in Plant Science 25, 141–147 (2020).
39. Chan, K. X., Phua, S. Y., Crisp, P., McQuinn, R. & Pogson, B. J. Learning the Languages of
the Chloroplast: Retrograde Signaling and Beyond. Annu. Rev. Plant Biol. 67, 25–53
(2016).
40. Fang, X. et al. Chloroplast-to-Nucleus Signaling Regulates MicroRNA Biogenesis in
Arabidopsis. Dev. Cell 48, 371-382.e4 (2019).
41. Sun, A. Z. & Guo, F. Q. Chloroplast retrograde regulation of heat stress responses in
plants. Frontiers in Plant Science 7, 398 (2016).
42. Greenham, K. & McClung, C. R. Integrating circadian dynamics with physiological
processes in plants. Nature Reviews Genetics 16, 598–610 (2015).
43. Ronald, J. & Davis, S. J. Focusing on the nuclear and subnuclear dynamics of light and
circadian signalling. Plant Cell and Environment 42, 2871–2884 (2019).
44. Burko, Y. et al. Chimeric Activators and Repressors Define HY5 Activity and Reveal a
Light-Regulated Feedback Mechanism. Plant Cell 32, tpc.00772.2019 (2020).
45. Holm, M., Ma, L. G., Qu, L. J. & Deng, X. W. Two interacting bZIP proteins are direct
targets of COP1-mediated control of light-dependent gene expression in Arabidopsis.
Genes Dev. 16, 1247–1259 (2002).
46. Osterlund, M. T., Hardtke, C. S., Wei, N. & Deng, X. W. Targeted destabilization of HY5
during light-regulated development of Arabidopsis. Nature 405, 462–466 (2000).
47. Huang, X., Ouyang, X. & Deng, X. W. Beyond repression of photomorphogenesis: Role
switching of COP/DET/FUS in light signaling. Current Opinion in Plant Biology 21, 96–
103 (2014).
48. Lau, K., Podolec, R., Chappuis, R., Ulm, R. & Hothorn, M. Plant photoreceptors and their
signaling components compete for COP 1 binding via VP peptide motifs.
EMBO J. 38, (2019).
49. Oravecz, A. et al. CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B
response in Arabidopsis. Plant Cell 18, 1975–1990 (2006).
50. Ren, H. et al. Two E3 ligases antagonistically regulate the UV-B response in Arabidopsis.
Proc. Natl. Acad. Sci. U. S. A. 116, 4722–4731 (2019).
51. Yang, Y. et al. UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl
elongation in Arabidopsis. Nat. Plants 4, 98–107 (2018).
52. Rai, N. et al. The photoreceptor UVR8 mediates the perception of both UV‐B and UV‐A
35
wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes.
Plant. Cell Environ. pce.13752 (2020). doi:10.1111/pce.13752
53. Toledo-Ortiz, G. et al. The HY5-PIF Regulatory Module Coordinates Light and
Temperature Control of Photosynthetic Gene Transcription. PLoS Genet. 10,
e1004416–e1004416 (2014).
54. Ling, J. J., Li, J., Zhu, D. & Deng, X. W. Noncanonical role of Arabidopsis COP1/SPA
complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in
darkness. Proc. Natl. Acad. Sci. U. S. A. 114, 3539–3544 (2017).
55. Pham, V. N., Kathare, P. K. & Huq, E. Dynamic regulation of PIF5 by COP1-SPA complex
to optimize photomorphogenesis in Arabidopsis. Plant J. 96, 260–273 (2018).
56. Dong, J. et al. Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively
regulating phytochrome-interacting factors in the dark. Plant Cell 26, 3630–3645
(2014).
57. Pepper, A., Delaney, T., Washburnt, T., Poole, D. & Chory, J. DET1, a negative regulator
of light-mediated development and gene expression in arabidopsis, encodes a novel
nuclear-localized protein. Cell 78, 109–116 (1994).
58. Schroeder, D. F. et al. De-etiolated 1 and damaged DNA binding protein 1 interact to
regulate Arabidopsis photomorphogenesis. Curr. Biol. 12, 1462–1472 (2002).
59. Castells, E. et al. The conserved factor DE-ETIOLATED 1 cooperates with CUL4-DDB1
DDB2 to maintain genome integrity upon UV stress. EMBO J. 30, 1162–1172 (2011).
60. Fonseca, S. & Rubio, V. Arabidopsis CRL4 Complexes: Surveying Chromatin States and
Gene Expression. Frontiers in Plant Science 10, 1095 (2019).
61. Park, E. et al. Degradation of Phytochrome Interacting Factor 3 in Phytochrome-
Mediated Light Signaling. Plant Cell Physiol. 45, 968–975 (2004).
62. Bauer, D. et al. Constitutive photomorphogenesis 1 and multiple phytoresectors
control degradation of phytochrome interacting factor 3, a transcription factor
required for light signaling in arabidopsis. Plant Cell 16, 1433–1445 (2004).
63. Sharma, A. et al. UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem
elongation in sunlight. Nat. Commun. 10, 1–10 (2019).
64. Al-Sady, B., Ni, W., Kircher, S., Schäfer, E. & Quail, P. H. Photoactivated Phytochrome
Induces Rapid PIF3 Phosphorylation Prior to Proteasome-Mediated Degradation. Mol.
Cell 23, 439–446 (2006).
36
65. Park, E. et al. Phytochrome B inhibits binding of phytochrome-interacting factors to
their target promoters. Plant J. 72, 537–546 (2012).
66. Shen, H. et al. Light-induced phosphorylation and degradation of the negative
regulator phytochrome-interacting factor1 from Arabidopsis depend upon its direct
physical interactions with photoactivated phytochromes. Plant Cell 20, 1586–1602
(2008).
67. Pedmale, U. V. et al. Cryptochromes Interact Directly with PIFs to Control Plant Growth
in Limiting Blue Light. Cell 164, 233–245 (2016).
68. Ma, D. et al. Cryptochrome 1 interacts with PIF4 to regulate high temperature-
mediated hypocotyl elongation in response to blue light. Proc. Natl. Acad. Sci. U. S. A.
113, 224–229 (2016).
69. Shi, H. et al. The Red Light Receptor Phytochrome B Directly Enhances Substrate-E3
Ligase Interactions to Attenuate Ethylene Responses. Dev. Cell 39, 597–610 (2016).
70. Liang, T. et al. UVR8 Interacts with BES1 and BIM1 to Regulate Transcription and
Photomorphogenesis in Arabidopsis. Dev. Cell 44, 512-523.e5 (2018).
71. Wu, J. et al. phyB Interacts with BES1 to Regulate Brassinosteroid Signaling in
Arabidopsis. Plant Cell Physiol. 60, 353–366 (2019).
72. Wang, W. et al. Photoexcited CRYPTOCHROME1 interacts with dephosphorylated bes1
to regulate brassinosteroid signaling and photomorphogenesis in arabidopsis. Plant
Cell 30, 1989–2005 (2018).
73. Liu, H. et al. Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral
initiation in Arabidopsis. Science (80-. ). 322, 1535–1539 (2008).
74. Lee, C. M. et al. Decoys untangle complicated redundancy and reveal targets of
circadian clock F-BOX proteins. Plant Physiol. 177, 1170–1186 (2018).
75. Kim, T. S., Wang, L., Kim, Y. J. & Somers, D. E. Compensatory Mutations in GI and ZTL
May Modulate Temperature Compensation in the Circadian Clock. Plant Physiol. 182,
1130–1141 (2020).
76. Yang, Y. et al. UV‐B photoreceptor UVR8 interacts with MYB73/MYB77 to regulate
auxin responses and lateral root development. EMBO J. 39, (2020).
77. Gould, P. D. et al. The molecular basis of temperature compensation in the Arabidopsis
circadian clock. Plant Cell 18, 1177–1187 (2006).
78. Antoniou-Kourounioti, R. L. et al. Temperature Sensing Is Distributed throughout the
37
Regulatory Network that Controls FLC Epigenetic Silencing in Vernalization. Cell Syst. 7,
643-655.e9 (2018).
79. Vu, L. D., Gevaert, K. & De Smet, I. Feeling the Heat: Searching for Plant Thermosensors.
Trends in Plant Science 24, 210–219 (2019).
80. Martinière, A. et al. Homeostasis of plasma membrane viscosity in fluctuating
temperatures. New Phytol. 192, 328–337 (2011).
81. Knight, H., Trewavas, A. J. & Knight, M. R. Cold calcium signaling in Arabidopsis involves
two cellular pools and a change in calcium signature after acclimation. Plant Cell 8,
489–503 (1996).
82. Gong, M., van der Luit, A. H., Knight, M. R. & Trewavas, A. J. Heat-Shock-Induced
Changes in Intracellular Ca 2+ Level in Tobacco Seedlings in Relation to
Thermotolerance. Plant Physiol. 116, 429–437 (1998).
83. Guo, X., Liu, D. & Chong, K. Cold signaling in plants: Insights into mechanisms and
regulation. J. Integr. Plant Biol. 60, 745–756 (2018).
84. Ding, Y., Shi, Y. & Yang, S. Molecular Regulation of Plant Responses to Environmental
Temperatures. Mol. Plant 13, 544–564 (2020).
85. Saidi, Y. et al. The Heat Shock Response in Moss Plants Is Regulated by Specific Calcium-
Permeable Channels in the Plasma Membrane. Plant Cell 21, 2829–2843 (2009).
86. Finka, A., Cuendet, A. F. H., Maathuis, F. J. M., Saidi, Y. & Goloubinoff, P. Plasma
Membrane Cyclic Nucleotide Gated Calcium Channels Control Land Plant Thermal
Sensing and Acquired Thermotolerance. Plant Cell 24, 3333–3348 (2012).
87. Casal, J. J. & Qüesta, J. I. Light and temperature cues: multitasking receptors and
transcriptional integrators. New Phytol. 217, (2018).
88. Fujii, Y. et al. Phototropin perceives temperature based on the lifetime of its
photoactivated state. Proc. Natl. Acad. Sci. 114, 9206–9211 (2017).
89. Li, B., Gao, K., Ren, H. & Tang, W. Molecular mechanisms governing plant responses to
high temperatures. J. Integr. Plant Biol. 60, 757–779 (2018).
90. Åkerfelt, M., Morimoto, R. I. & Sistonen, L. Heat shock factors: integrators of cell stress,
development and lifespan. Nat. Rev. Mol. Cell Biol. 11, 545–555 (2010).
91. Chung, B. Y. W. et al. An RNA thermoswitch regulates daytime growth in Arabidopsis.
Nat. Plants 6, 522–532 (2020).
92. Kumar, S. V & Wigge, P. A. H2A.Z-containing nucleosomes mediate the thermosensory
38
response in Arabidopsis. Cell 140, 136–147 (2010).
93. Cortijo, S. et al. Transcriptional Regulation of the Ambient Temperature Response by
H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. Mol. Plant 10,
1258–1273 (2017).
94. del Olmo, I., Poza‐Viejo, L., Piñeiro, M., Jarillo, J. A. & Crevillén, P. High ambient
temperature leads to reduced FT expression and delayed flowering in
Brassica rapa via a mechanism associated with H2A.Z dynamics. Plant J. 100, 343–356
(2019).
95. Zhao, Y., Antoniou-Kourounioti, R. L., Calder, G., Dean, C. & Howard, M. Temperature-
dependent growth contributes to long-term cold sensing. Nature 583, 825–829 (2020).
96. Quint, M. et al. Molecular and genetic control of plant thermomorphogenesis. Nature
Plants 2, 1–9 (2016).
97. Kumar, S. V et al. Transcription factor PIF4 controls the thermosensory activation of
flowering. Nature 484, 242–245 (2012).
98. Crawford, A. J., McLachlan, D. H., Hetherington, A. M. & Franklin, K. A. High
temperature exposure increases plant cooling capacity. Current Biology 22, R396–R397
(2012).
99. Li, B., Gao, Z., Liu, X., Sun, D. & Tang, W. Transcriptional profiling reveals a time-of-day-
specific role of REVEILLE 4/8 in regulating the first wave of heat shock–induced gene
expression in Arabidopsis. Plant Cell 31, 2353–2369 (2019).
100. Yamada, K. et al. Cytosolic HSP90 Regulates the Heat Shock Response That Is
Responsible for Heat Acclimation in Arabidopsis thaliana. J. Biol. Chem. 282, 37794–
37804 (2007).
101. Hahn, A., Bublak, D., Schleiff, E. & Scharf, K.-D. Crosstalk between Hsp90 and Hsp70
Chaperones and Heat Stress Transcription Factors in Tomato. Plant Cell 23, 741–755
(2011).
102. Ohama, N., Sato, H., Shinozaki, K. & Yamaguchi-Shinozaki, K. Transcriptional Regulatory
Network of Plant Heat Stress Response. Trends Plant Sci. 22, 53–65 (2017).
103. Toorop, P. E., Barroco, R. M., Engler, G., Groot, S. P. C. & Hilhorst, H. W. M. Differentially
expressed genes associated with dormancy or germination of Arabidopsis thaliana
seeds. Planta 221, 637–647 (2005).
104. Lim, S. et al. ABA-insensitive3, ABA-insensitive5, and DELLAs interact to activate the
39
expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds
in Arabidopsis. Plant Cell 25, 4863–4878 (2013).
105. Gan, E. S. et al. Jumonji demethylases moderate precocious flowering at elevated
temperature via regulation of FLC in Arabidopsis. Nat. Commun. 5, 1–13 (2014).
106. Koini, M. A. et al. High Temperature-Mediated Adaptations in Plant Architecture
Require the bHLH Transcription Factor PIF4. Curr. Biol. 19, 408–413 (2009).
107. Fiorucci, A.-S. et al. PHYTOCHROME INTERACTING FACTOR 7 is important for early
responses to elevated temperature in Arabidopsis seedlings. New Phytol. 226, 50–58
(2020).
108. Ezer, D. et al. The evening complex coordinates environmental and endogenous signals
in Arabidopsis. Nat. Plants 3, 17087 (2017).
109. Tasset, C. et al. POWERDRESS-mediated histone deacetylation is essential for
thermomorphogenesis in Arabidopsis thaliana. PLOS Genet. 14, e1007280–e1007280
(2018).
110. Sun, Q. et al. SHB1 and CCA1 interaction desensitizes light responses and enhances
thermomorphogenesis. Nat. Commun. 10, 3110 (2019).
111. Ibañez, C. et al. Brassinosteroids Dominate Hormonal Regulation of Plant
Thermomorphogenesis via BZR1. Curr. Biol. 28, 303-310.e3 (2018).
112. Han, X. et al. Arabidopsis Transcription Factor TCP5 Controls Plant
Thermomorphogenesis by Positively Regulating PIF4 Activity. iScience 15, 611–622
(2019).
113. Hayes, S. et al. UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant
Thermomorphogenesis. Curr. Biol. 27, 120–127 (2017).
114. Delker, C. et al. The DET1-COP1-HY5 Pathway Constitutes a Multipurpose Signaling
Module Regulating Plant Photomorphogenesis and Thermomorphogenesis. Cell Rep. 9,
1983–1989 (2014).
115. Park, Y.-J., Lee, H.-J., Ha, J.-H., Kim, J. Y. & Park, C.-M. COP1 conveys warm temperature
information to hypocotyl thermomorphogenesis. New Phytol. 215, 269–280 (2017).
116. Gangappa, S. N., Berriri, S. & Kumar, S. V. PIF4 Coordinates Thermosensory Growth and
Immunity in Arabidopsis. Curr. Biol. 27, 243–249 (2017).
117. Franklin, K. A. et al. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) regulates auxin
biosynthesis at high temperature. Proc. Natl. Acad. Sci. 108, 20231–20235 (2011).
40
118. Sun, J., Qi, L., Li, Y., Chu, J. & Li, C. PIF4–Mediated Activation of YUCCA8 Expression
Integrates Temperature into the Auxin Pathway in Regulating Arabidopsis Hypocotyl
Growth. PLoS Genet. 8, e1002594 (2012).
119. Sun, J., Qi, L., Li, Y., Zhai, Q. & Li, C. PIF4 and PIF5 transcription factors link blue light
and auxin to regulate the phototropic response in Arabidopsis. Plant Cell 25, 2102–
2114 (2013).
120. Bellstaedt, J. et al. A mobile auxin signal connects temperature sensing in cotyledons
with growth responses in hypocotyls. Plant Physiol. 180, 757–766 (2019).
121. Kim, S. et al. The epidermis coordinates thermoresponsive growth through the phyB-
PIF4-auxin pathway. Nat. Commun. 11, 1–13 (2020).
122. Catala, R., Medina, J. & Salinas, J. Integration of low temperature and light signaling
during cold acclimation response in Arabidopsis. Proc. Natl. Acad. Sci. 108, 16475–
16480 (2011).
123. Jia, Y. et al. The cbfs triple mutants reveal the essential functions of CBFs in cold
acclimation and allow the definition of CBF regulons in Arabidopsis. New Phytol. 212,
345–353 (2016).
124. Zhao, C. et al. Mutational Evidence for the Critical Role of CBF Genes in Cold
Acclimation in Arabidopsis. Plant Physiol. pp.00533.2016-p.00533.2016 (2016).
doi:10.1104/pp.16.00533
125. Chinnusamy, V. ICE1: a regulator of cold-induced transcriptome and freezing tolerance
in Arabidopsis. Genes Dev. 17, 1043–1054 (2003).
126. Fursova, O. V, Pogorelko, G. V & Tarasov, V. A. Identification of ICE2, a gene involved
in cold acclimation which determines freezing tolerance in Arabidopsis thaliana. Gene
429, 98–103 (2009).
127. Ding, Y. et al. OST1 Kinase Modulates Freezing Tolerance by Enhancing ICE1 Stability in
Arabidopsis. Dev. Cell 32, 278–289 (2015).
128. Ding, Y. et al. EGR 2 phosphatase regulates OST 1 kinase
activity and freezing tolerance in Arabidopsis. EMBO J. 38, (2019).
129. Ding, Y. et al. OST 1‐mediated BTF 3L phosphorylation
positively regulates CBF s during plant cold responses. EMBO J. 37, (2018).
130. Liu, Z. et al. Plasma Membrane CRPK1-Mediated Phosphorylation of 14-3-3 Proteins
Induces Their Nuclear Import to Fine-Tune CBF Signaling during Cold Response. Mol
41
Cell 66, 117-128 e5 (2017).
131. Li, H. et al. MPK3- and MPK6-Mediated ICE1 Phosphorylation Negatively Regulates ICE1
Stability and Freezing Tolerance in Arabidopsis. Dev. Cell 43, 630-642.e4 (2017).
132. Ye, K. et al. BRASSINOSTEROID-INSENSITIVE2 Negatively Regulates the Stability of
Transcription Factor ICE1 in Response to Cold Stress in Arabidopsis. Plant Cell
tpc.00058.2019-tpc.00058.2019 (2019). doi:10.1105/tpc.19.00058
133. Bouché, F., Woods, D. P. & Amasino, R. M. Winter Memory throughout the Plant
Kingdom: Different Paths to Flowering. Plant Physiol. 173, 27–35 (2017).
134. Michaels, S. D. & Amasino, R. M. FLOWERING LOCUS C encodes a novel MADS domain
protein that acts as a repressor of flowering. Plant Cell 11, 949–956 (1999).
135. Sheldon, C. C., Conn, A. B., Dennis, E. S. & Peacock, W. J. Different regulatory regions
are required for the vernalization-induced repression of FLOWERING LOCUS C and for
the epigenetic maintenance of repression. Plant Cell 14, 2527–2537 (2002).
136. Hepworth, J. et al. Absence of warmth permits epigenetic memory of winter in
Arabidopsis. Nat. Commun. (2018). doi:10.1038/s41467-018-03065-7
137. Andres, F. & Coupland, G. The genetic basis of flowering responses to seasonal cues.
Nat Rev Genet 13, 627–639 (2012).
138. Hepworth, J. & Dean, C. Flowering Locus C’s Lessons: Conserved Chromatin Switches
Underpinning Developmental Timing and Adaptation. Plant Physiol. 168, 1237–1245
(2015).
139. Hiller, M., Zhang, Z., Backofen, R. & Stamm, S. Pre-mRNA Secondary Structures
Influence Exon Recognition. PLoS Genet. 3, e204 (2007).
140. Erhard, K. F., Talbot, J. E. R. B., Deans, N. C., McClish, A. E. & Hollick, J. B. Nascent
transcription affected by RNA polymerase IV in Zea mays. Genetics 199, 1107–1125
(2015).
141. Hetzel, J., Duttke, S. H., Benner, C. & Chory, J. Nascent RNA sequencing reveals distinct
features in plant transcription. Proc Natl Acad Sci U S A 113, 12316–12321 (2016).
142. Liu, W. et al. RNA-directed DNA methylation involves co-transcriptional small-RNA-
guided slicing of polymerase v transcripts in Arabidopsis. Nat. Plants 4, 181–188 (2018).
143. Zhu, J., Liu, M., Liu, X. & Dong, Z. RNA polymerase II activity revealed by GRO-seq and
pNET-seq in Arabidopsis. Nat. Plants 4, 1112–1123 (2018).
144. Leng, X. et al. Organismal benefits of transcription speed control at gene boundaries.
42
EMBO Rep. (2020). doi:10.15252/embr.201949315
145. Kindgren, P., Ivanov, M. & Marquardt, S. Native elongation transcript sequencing
reveals temperature dependent dynamics of nascent RNAPII transcription in
Arabidopsis. Nucleic Acids Res. (2019). doi:10.1093/nar/gkz1189
146. Calixto, C. P. G. et al. Rapid and dynamic alternative splicing impacts the arabidopsis
cold response transcriptome[CC-BY]. Plant Cell 30, 1424–1444 (2018).
147. Calixto, C. P. G. et al. Cold-dependent expression and alternative splicing of arabidopsis
long non-coding RNAs. Front. Plant Sci. 10, (2019).
148. Mano, S., Hayashi, M. & Nishimura, M. Light regulates alternative splicing of
hydroxypyruvate reductase in pumpkin. Plant J. 17, 309–320 (1999).
149. Pose, D. et al. Temperature-dependent regulation of flowering by antagonistic FLM
variants. Nature 503, 414–417 (2013).
150. Sureshkumar, S., Dent, C., Seleznev, A., Tasset, C. & Balasubramanian, S. Nonsense-
mediated mRNA decay modulates FLM-dependent thermosensory flowering response
in Arabidopsis. Nat. Plants 2, 1–7 (2016).
151. Kim, G.-D., Yoo, S.-D. & Cho, Y.-H. STABILIZED1 as a heat stress-specific splicing factor
in Arabidopsis thaliana. Plant Signal. Behav. 13, e1432955 (2018).
152. Lee, B. H., Kapoor, A., Zhu, J. & Zhu, J. K. Stabilized1, a stress-upregulated nuclear
protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in
Arabidopsis. Plant Cell 18, 1736–1749 (2006).
153. Vihervaara, A., Duarte, F. M. & Lis, J. T. Molecular mechanisms driving transcriptional
stress responses. Nature Reviews Genetics 19, 385–397 (2018).
154. Simpson, C. G. et al. Monitoring changes in alternative precursor messenger RNA
splicing in multiple gene transcripts. Plant J. 53, 1035–1048 (2007).
155. Kurihara, Y. et al. Transcripts from downstream alternative transcription start sites
evade uORF-mediated inhibition of gene expression in Arabidopsis. Proc. Natl. Acad.
Sci. U. S. A. 115, 7831–7836 (2018).
156. Cheng, Y.-L. & Tu, S.-L. Alternative Splicing and Cross-Talk with Light Signaling. Plant
Cell Physiol. 59, 1104–1110 (2018).
157. Tanabe, N., Yoshimura, K., Kimura, A., Yabuta, Y. & Shigeoka, S. Differential Expression
of Alternatively Spliced mRNAs of Arabidopsis SR Protein Homologs, atSR30 and
atSR45a, in Response to Environmental Stress. Plant Cell Physiol. 48, 1036–1049
43
(2007).
158. Petrillo, E. et al. A chloroplast retrograde signal regulates nuclear alternative splicing.
Science (80-. ). 344, 427–430 (2014).
159. Tognacca, R. S. et al. Alternative Splicing Regulation During Light-Induced Germination
of Arabidopsis thaliana Seeds. Front. Plant Sci. 10, 1076 (2019).
160. Mancini, E. et al. Acute Effects of Light on Alternative Splicing in Light-Grown Plants.
Photochem. Photobiol. 92, 126–133 (2016).
161. Shikata, H. et al. Phytochrome controls alternative splicing to mediate light responses
in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 111, 18781–18786 (2014).
162. Xin, R., Kathare, P. K. & Huq, E. Coordinated Regulation of Pre-mRNA Splicing by the
SFPS-RRC1 Complex to Promote Photomorphogenesis. Plant Cell 31, 2052–2069
(2019).
163. Ushijima, T. et al. Light Controls Protein Localization through Phytochrome-Mediated
Alternative Promoter Selection. Cell 171, 1316-1325.e12 (2017).
164. Zhang, H., Wang, Y. & Lu, J. Function and Evolution of Upstream ORFs in Eukaryotes.
Trends in Biochemical Sciences 44, 782–794 (2019).
165. Hartmann, L. et al. Alternative splicing substantially diversifies the transcriptome
during early photomorphogenesis and correlates with the energy availability in
arabidopsis. Plant Cell 28, 2715–2734 (2016).
166. Godoy Herz, M. A. et al. Light Regulates Plant Alternative Splicing through the Control
of Transcriptional Elongation. Mol. Cell 73, 1066-1074.e3 (2019).
167. Shikata, H. et al. The RS domain of Arabidopsis splicing factor RRC1 is required for
phytochrome B signal transduction. Plant J. 70, 727–738 (2012).
168. Wu, H. P. et al. Genome-wide analysis of light-regulated alternative splicing mediated
by photoreceptors in Physcomitrella patens. Genome Biol. 15, R10 (2013).
169. Xin, R. et al. SPF45-related splicing factor for phytochrome signaling promotes
photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis. Proc. Natl. Acad.
Sci. U. S. A. 114, E7018–E7027 (2017).
170. Dong, J., Chen, H., Deng, X. W., Irish, V. F. & Wei, N. Phytochrome B Induces Intron
Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR3.
Plant Physiol. 182, 159–166 (2020).
171. Shih, C. J. et al. Heterogeneous nuclear ribonucleoprotein h1 coordinates with
44
phytochrome and the U1 snRNP complex to regulate alternative splicing in
physcomitrella patens. Plant Cell 31, 2510–2524 (2019).
172. Lin, B. Y., Shih, C. J., Hsieh, H. Y., Chen, H. C. & Tu, S. L. Phytochrome Coordinates with
a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer. Plant Physiol.
182, 243–254 (2020).
173. Ma, Y., Gil, S., Grasser, K. D. & Mas, P. Targeted Recruitment of the Basal Transcriptional
Machinery by LNK Clock Components Controls the Circadian Rhythms of Nascent RNAs
in Arabidopsis. Plant Cell (2018). doi:10.1105/tpc.18.00052
174. Rugnone, M. L. et al. LNK genes integrate light and clock signaling networks at the core
of the Arabidopsis oscillator. Proc. Natl. Acad. Sci. U. S. A. 110, 12120–12125 (2013).
175. Csorba, T., Questa, J. I., Sun, Q. & Dean, C. Antisense COOLAIR mediates the
coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad
Sci U S A 111, 16160–16165 (2014).
176. Swiezewski, S., Liu, F., Magusin, A. & Dean, C. Cold-induced silencing by long antisense
transcripts of an Arabidopsis Polycomb target. Nature 462, 799–802 (2009).
177. Rosa, S., Duncan, S. & Dean, C. Mutually exclusive sense-antisense transcription at FLC
facilitates environmentally induced gene repression. Nat Commun 7, 13031 (2016).
178. Kim, D. H. & Sung, S. Vernalization-Triggered Intragenic Chromatin Loop Formation by
Long Noncoding RNAs. Dev Cell 40, 302-312 e4 (2017).
179. Heo, J. B. & Sung, S. Vernalization-mediated epigenetic silencing by a long intronic
noncoding RNA. Science (80-. ). 331, 76–79 (2011).
180. Zhao, X. et al. Global identification of Arabidopsis lncRNAs reveals the regulation of
MAF4 by a natural antisense RNA. Nat. Commun. 9, 1–12 (2018).
181. Kim, D. H. & Sung, S. Coordination of the vernalization response through a VIN3 and
FLC gene family regulatory network in Arabidopsis. Plant Cell 25, 454–469 (2013).
182. Kindgren, P., Ard, R., Ivanov, M. & Marquardt, S. Transcriptional read-through of the
long non-coding RNA SVALKA governs plant cold acclimation. Nat. Commun. 9, 1–11
(2018).
183. Niehrs, C. & Luke, B. Regulatory R-loops as facilitators of gene expression and genome
stability. Nature Reviews Molecular Cell Biology 21, 167–178 (2020).
184. Hegazy, Y. A., Fernando, C. M. & Tran, E. J. The balancing act of R-loop biology: The
good, the bad, and the ugly. Journal of Biological Chemistry 295, 905–913 (2020).
45
185. Crossley, M. P., Bocek, M. & Cimprich, K. A. R-Loops as Cellular Regulators and Genomic
Threats. Molecular Cell 73, 398–411 (2019).
186. Belotserkovskii, B. P., Tornaletti, S., D’Souza, A. D. & Hanawalt, P. C. R-loop generation
during transcription: Formation, processing and cellular outcomes. DNA Repair 71, 69–
81 (2018).
187. Sun, Q., Csorba, T., Skourti-Stathaki, K., Proudfoot, N. J. & Dean, C. R-loop stabilization
represses antisense transcription at the Arabidopsis FLC locus. Science (80-. ). 340, 619–
621 (2013).
188. Ariel, F. et al. R-Loop Mediated trans Action of the APOLO Long Noncoding RNA. Mol.
Cell 77, 1055-1065.e4 (2020).
189. Xu, W. et al. The R-loop Atlas of Arabidopsis Development and Responses to
Environmental Stimuli. Plant Cell 32, tpc.00802.2019 (2020).
190. Wang, Y. et al. Arabidopsis noncoding RNA mediates control of photomorphogenesis
by red light. Proc Natl Acad Sci U S A 111, 10359–10364 (2014).
191. McClung, C. R. & Davis, S. J. Ambient thermometers in plants: From physiological
outputs towards mechanisms of thermal sensing. Current Biology 20, R1086–R1092
(2010).
192. Kaiserli, E., Perrella, G. & Davidson, M. L. Light and temperature shape nuclear
architecture and gene expression. Current Opinion in Plant Biology 45, 103–111 (2018).
193. Lindquist, S. The Heat-Shock Response. Annu. Rev. Biochem. 55, 1151–1191 (1986).
194. Pecinka, A. et al. Epigenetic regulation of repetitive elements is attenuated by
prolonged heat stress in Arabidopsis. Plant Cell 22, 3118–3129 (2010).
195. Wang, L.-C. et al. Arabidopsis HIT4 encodes a novel chromocentre-localized protein
involved in the heat reactivation of transcriptionally silent loci and is essential for heat
tolerance in plants. J. Exp. Bot. 64, 1689–1701 (2013).
196. Sullivan, A. M. et al. Mapping and dynamics of regulatory DNA and transcription factor
networks in A. thaliana. Cell Rep. 8, 2015–2030 (2014).
197. Wang, L. C., Wu, J. R., Hsu, Y. J. & Wu, S. J. Arabidopsis HIT4, a regulator involved in
heat-triggered reorganization of chromatin and release of transcriptional gene
silencing, relocates from chromocenters to the nucleolus in response to heat stress.
New Phytol. 205, 544–554 (2015).
198. Tessadori, F., Schulkes, R. K., Driel, R. van & Fransz, P. Light-regulated large-scale
46
reorganization of chromatin during the floral transition in Arabidopsis. Plant J. 50, 848–
857 (2007).
199. Bourbousse, C. et al. Light signaling controls nuclear architecture reorganization during
seedling establishment. Proc. Natl. Acad. Sci. U. S. A. 112, E2836–E2844 (2015).
200. Bourbousse, C., Barneche, F. & Laloi, C. Plant Chromatin Catches the Sun. Frontiers in
Plant Science 10, 1728 (2020).
201. Perrella, G., Zioutopoulou, A., Headland, L. R. & Kaiserli, E. The impact of light and
temperature on chromatin organisation and plant adaptation.
doi:10.1093/jxb/eraa154/5811687
202. Benvenuto, G., Formiggini, F., Laflamme, P., Malakhov, M. & Bowler, C. The
photomorphogenesis regulator DET1 binds the amino-terminal tail of histone H2B in a
nucleosome context. Curr. Biol. 12, 1529–1534 (2002).
203. Bourbousse, C. et al. Histone H2B Monoubiquitination Facilitates the Rapid Modulation
of Gene Expression during Arabidopsis Photomorphogenesis. PLoS Genet. 8, e1002825
(2012).
204. Nassrallah, A. et al. DET1-mediated degradation of a SAGA-like deubiquitination
module controls H2Bub homeostasis. Elife 7, (2018).
205. Zhao, C. et al. Temperature increase reduces global yields of major crops in four
independent estimates. Proc. Natl. Acad. Sci. U. S. A. 114, 9326–9331 (2017).
206. Van Der Woude, L. C. et al. HISTONE DEACETYLASE 9 stimulates auxin-dependent
thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion. Proc.
Natl. Acad. Sci. U. S. A. 116, 25343–25354 (2019).
207. Pajoro, A., Severing, E., Angenent, G. C. & Immink, R. G. H. Histone H3 lysine 36
methylation affects temperature-induced alternative splicing and flowering in plants.
Genome Biol 18, 102 (2017).
208. Charron, J. B. F., He, H., Elling, A. A. & Denga, X. W. Dynamic landscapes of four histone
modifications during deetiolation in arabidopsis. Plant Cell 21, 3732–3748 (2009).
209. Peng, M. et al. Linking phytochrome-interacting factor to histone modification in plant
shade avoidance. Plant Physiol. 176, 1341–1351 (2018).
210. Yang, C. et al. HY5-HDA9 Module Transcriptionally Regulates Plant Autophagy in
Response to Light-to-Dark Conversion and Nitrogen Starvation. Mol. Plant 13, 515–531
(2020).
47
211. Liu, X. et al. PHYTOCHROME INTERACTING FACTOR3 associates with the histone
deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in
etiolated Arabidopsis seedlings. Plant Cell 25, 1258–1273 (2013).
212. Gu, D. et al. Identification of HDA15-PIF1 as a key repression module directing the
transcriptional network of seed germination in the dark. Nucleic Acids Res. 45, 7137–
7150 (2017).
213. Zhang, D., Li, Y., Zhang, X., Zha, P. & Lin, R. The SWI2/SNF2 Chromatin-Remodeling
ATPase BRAHMA Regulates Chlorophyll Biosynthesis in Arabidopsis. Mol. Plant 10,
155–167 (2017).
214. Lee, N., Kang, H., Lee, D. & Choi, G. A histone methyltransferase inhibits seed
germination by increasing PIF1 mRNA expression in imbibed seeds. Plant J. 78, 282–
293 (2014).
215. Cho, J. N. et al. Control of Seed Germination by Light-Induced Histone Arginine
Demethylation Activity. Dev. Cell 22, 736–748 (2012).
216. Jones, M. A., Morohashi, K., Grotewold, E. & Harmer, S. L. Arabidopsis JMJD5/JMJ30
Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable
Temperature Compensation. Front. Plant Sci. 10, 57 (2019).
217. Zha, P., Jing, Y., Xu, G. & Lin, R. PICKLE chromatin-remodeling factor controls
thermosensory hypocotyl growth of Arabidopsis. Plant. Cell Environ. 40, 2426–2436
(2017).
218. Jing, Y. et al. Arabidopsis chromatin remodeling factor PICKLE interacts with
transcription factor HY5 to regulate hypocotyl cell elongation. Plant Cell 25, 242–256
(2013).
219. Friedrich, T., Faivre, L., Bäurle, I. & Schubert, D. Chromatin-based mechanisms of
temperature memory in plants. Plant. Cell Environ. 42, 762–770 (2019).
220. Costa, S. & Dean, C. Storing memories: the distinct phases of Polycomb-mediated
silencing of Arabidopsis FLC. (2019). doi:10.1042/BST20190255
221. Shindo, C., Lister, C., Crevillen, P., Nordborg, M. & Dean, C. Variation in the epigenetic
silencing of FLC contributes to natural variation in Arabidopsis vernalization response.
Genes Dev 20, 3079–3083 (2006).
222. Questa, J. I. et al. Arabidopsis transcriptional repressor VAL1 triggers Polycomb
silencing at FLC during vernalization. Science (80-. ). 353, 485–488 (2016).
48
223. Yuan, W. et al. A cis cold memory element and a trans epigenome reader mediate
Polycomb silencing of FLC by vernalization in Arabidopsis. Nat Genet 48, 1527–1534
(2016).
224. De Lucia, F., Crevillen, P., Jones, A. M., Greb, T. & Dean, C. A PHD-polycomb repressive
complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad
Sci U S A 105, 16831–16836 (2008).
225. Finnegan, E. J. & Dennis, E. S. Vernalization-Induced Trimethylation of Histone H3
Lysine 27 at FLC Is Not Maintained in Mitotically Quiescent Cells. Curr. Biol. 17, 1978–
1983 (2007).
226. Angel, A., Song, J., Dean, C. & Howard, M. A Polycomb-based switch underlying
quantitative epigenetic memory. Nature 476, 105–108 (2011).
227. Berry, S., Hartley, M., Olsson, T. S., Dean, C. & Howard, M. Local chromatin
environment of a Polycomb target gene instructs its own epigenetic inheritance. Elife
4, (2015).
228. Yang, H. et al. Distinct phases of Polycomb silencing to hold epigenetic memory of cold
in Arabidopsis. Science (80-. ). (2017). doi:10.1126/science.aan1121
229. Angel, A. et al. Vernalizing cold is registered digitally at FLC. Proc. Natl. Acad. Sci. U. S.
A. 112, (2015).
230. Qüesta, J. I. et al. Noncoding SNPs influence a distinct phase of Polycomb silencing to
destabilize long-term epigenetic memory at Arabidopsis FLC. Genes Dev. 34, 446–461
(2020).
231. Yang, H., Howard, M. & Dean, C. Antagonistic roles for H3K36me3 and H3K27me3 in
the cold-induced epigenetic switch at Arabidopsis FLC. Curr Biol 24, 1793–1797 (2014).
232. Byun, Y. J., Koo, M. Y., Joo, H. J., Ha-Lee, Y. M. & Lee, D. H. Comparative analysis of gene
expression under cold acclimation, deacclimation and reacclimation in Arabidopsis.
Physiol. Plant. 152, 256–274 (2014).
233. Zuther, E. et al. Molecular signatures of increased freezing tolerance due to low
temperature memory in Arabidopsis. Plant. Cell Environ. 42, pce.13502 (2018).
234. Kwon, C. S., Lee, D., Choi, G. & Chung, W.-I. Histone occupancy-dependent and -
independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis.
Plant J. 60, 112–121 (2009).
235. Schubert, D. et al. Silencing by plant Polycomb-group genes requires dispersed
49
trimethylation of histone H3 at lysine 27. EMBO J. 25, 4638–4649 (2006).
236. Vyse, K. et al. Transcriptional and Post-Transcriptional Regulation and Transcriptional
Memory of Chromatin Regulators in Response to Low Temperature. Front. Plant Sci.
11, 39 (2020).
237. Mittler, R., Finka, A. & Goloubinoff, P. How do plants feel the heat? Trends in
Biochemical Sciences 37, 118–125 (2012).
238. Stief, A. et al. Arabidopsis miR156 regulates tolerance to recurring environmental
stress through SPL transcription factors. Plant Cell 26, 1792–1807 (2014).
239. Lämke, J., Brzezinka, K., Altmann, S. & Bäurle, I. A hit‐and‐run heat shock factor governs
sustained histone methylation and transcriptional stress memory. EMBO J. 35, 162–
175 (2016).
240. Brzezinka, K. et al. Arabidopsis FORGETTER1 mediates stress-induced chromatin
memory through nucleosome remodeling. Elife 5, (2016).
241. Ding, Y., Fromm, M. & Avramova, Z. Multiple exposures to drought ‘train’
transcriptional responses in Arabidopsis. Nat. Commun. 3, 1–9 (2012).
242. Feng, X. J. et al. Light affects salt stress-induced transcriptional memory of P5CS1 in
Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 113, E8335–E8343 (2016).
243. Martínez-García, J. F. & Moreno-Romero, J. Shedding light on the chromatin changes
that modulate shade responses. Physiol. Plant. (2020). doi:10.1111/ppl.13101
244. Gordon, M. J., Carmody, M., Albrecht, V. & Pogson, B. Systemic and local responses to
repeated HL stress-induced retrograde signaling in Arabidopsis. Front. Plant Sci. 3, 303
(2013).
245. Rossel, J. B. et al. Systemic and intracellular responses to photooxidative stress in
Arabidopsis. Plant Cell 19, 4091–4110 (2007).
246. Szechyńska-Hebda, M., Kruk, J., Górecka, M., Karpińska, B. & Karpiński, S. Evidence for
light wavelength-specific photoelectrophysiological signaling and memory of excess
light episodes in Arabidopsis. Plant Cell 22, 2201–2218 (2010).
247. Ganguly, D. R., Crisp, P. A., Eichten, S. R. & Pogson, B. J. Maintenance of pre-existing
DNA methylation states through recurring excess-light stress. Plant. Cell Environ. 41,
1657–1672 (2018).
248. Crisp, P. A. et al. Rapid recovery gene downregulation during excess-light stress and
recovery in arabidopsis. Plant Cell 29, 1836–1863 (2017).
50
249. Topham, A. T. et al. Temperature variability is integrated by a spatially embedded
decision-making center to break dormancy in Arabidopsis seeds. Proc. Natl. Acad. Sci.
U. S. A. 114, 6629–6634 (2017).
250. Burghardt, L. T., Edwards, B. R. & Donohue, K. Multiple paths to similar germination
behavior in Arabidopsis thaliana. New Phytol. 209, 1301–1312 (2016).
251. Chew, Y. H. et al. Mathematical models light up plant signaling. Plant Cell 26, 5–20
(2014).
51