Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition
Tremblay, Benjamin Jean-Marie (Centre de Recerca en Agrigenòmica)
Santini, Cristina P. (Centre de Recerca en Agrigenòmica)
Cheng, Yajiao (Centre de Recerca en Agrigenòmica)
Zhang, Xue (Swedish University of Agricultural Sciences. Plant Biology Department)
Rosa, Stefanie (Swedish University of Agricultural Sciences. Plant Biology Department)
Qüesta, Julia I. (Centre de Recerca en Agrigenòmica)

Date:	2024
Abstract:	Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.
Grants:	"la Caixa" Foundation 100010434 Ministerio de Economía y Competitividad SEV-2015-0533 Agencia Estatal de Investigación EUR2021-122003 Agencia Estatal de Investigación PID2019-110510GA-I00 Agencia Estatal de Investigación PRE2019-090156
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Plant development ; Reprogramming ; Long non-coding RNAs ; Epigenetics
Published in:	Nature communications, Vol. 15 (February 2024) , art. 1724, ISSN 2041-1723

DOI: 10.1038/s41467-024-46082-5
PMID: 38409232

21 p, 3.0 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles