RT Journal
A1 Sequeira-Mendes, Joana
A1 Vergara, Zaida
A1 Peiró, Ramon
A1 Morata, Jordi
A1 Aragüez, Irene
A1 Costas, Celina
A1 Mendez-Giraldez, Raul
A1 Casacuberta, Josep M.
A1 Bastolla, Ugo
A1 Gutierrez, Crisanto
T1 Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
JF Genome Research 
JO Genome Research 
YR 2019 
FD May 01 
VO 29 
IS 5 
SP 784 
OP 797 
DO 10.1101/gr.240986.118 
UL http://genome.cshlp.org/content/29/5/784.abstract 
AB 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.