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Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
Sequeira-Mendes, Joana (Centro de Biología Molecular Severo Ochoa)
Vergara, Zaida (Centro de Biología Molecular Severo Ochoa)
Peiró, Ramon (Centro de Biología Molecular Severo Ochoa)
Morata, Jordi (Centre de Recerca en Agrigenòmica)
Aragüez, Irene (Centro de Biología Molecular Severo Ochoa)
Costas, Celina (Centro de Biología Molecular Severo Ochoa)
Méndez Giráldez, Raúl (Centro de Biología Molecular Severo Ochoa)
Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica)
Bastolla, Ugo (Centro de Biología Molecular Severo Ochoa)
Gutiérrez, Crisanto (Centro de Biología Molecular Severo Ochoa)

Date: 2019
Abstract: Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have identified a set of ORIs of Arabidopsis thaliana and their chromatin landscape at two stages of post-embryonic development. ORIs associate with multiple chromatin signatures including transcription start sites (TSS) but also proximal and distal regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin, but at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the set of ORIs active in an organism at the post-embryo stage that should allow us to study ORI biology in response to development, environment, and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.
Note: Número d'acord de subvenció MINECO/BFU2012-34821
Note: Número d'acord de subvenció MINECO/BIO2013-50098-EXP
Note: Número d'acord de subvenció MINECO/BFU2015-68396-R
Note: Número d'acord de subvenció MINECO/BIO2016-79043-P
Note: Número d'acord de subvenció MINECO/AGL2013-43244-R
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, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. Creative Commons
Language: Anglès.
Document: article ; recerca ; acceptedVersion
Subject: DNA replication origin ; Nascent strands ; Cell cycle ; Gene expression ; Chromatin ; Heterochromatin ; Epigenetics ; Eukaryote ; Arabidopsis
Published in: Genome research, Vol. 29, Issue 5 (May 2019) , p. 784-797, ISSN 1549-5469

DOI: 10.1101/gr.240986.118
PMID: 30846531


Available from: 2019-11-30
Postprint

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

 Record created 2019-07-17, last modified 2019-08-12



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