GSE109668
DNA replication origins in whole Arabidopsis seedlings
Full genome replication in eukaryotes depends on the function of thousands of DNA replication origins (ORIs). The genome-wide identification of ORI location, achieved for animal and plant cells in culture, has been important to define their DNA and chromatin features. A major challenge in the field is to approach the biology of ORIs in whole organisms to understand their developmental plasticity. Here, we have determined the ORI location, activity and chromatin landscape in two developmental stages of Arabidopsis thaliana. We found that ORIs associate with multiple chromatin signatures including the most frequent at TSS but also at proximal and distal gene regulatory regions or repressed Polycomb domains. In constitutive heterochromatin, a high fraction of ORIs colocalize with GC-rich retrotransposons. Quantitative analysis of ORI activity led us to conclude that strong ORIs possess high scores of local GC content and clusters of GGN trinucleotides that may form G quadruplexes and other G-rich structures. We also found that development primarily influences ORI firing strength rather than the location of ORIs in different genomic loci. Moreover, ORIs that preferentially fire at early vegetative stages colocalize with GC-rich heterochromatin whereas those at later stages associate with transcribed genes. Our results provide the first identification of ORI features in a whole organism, opening new ways of studying DNA replication in different cell types in the context of development under normal and mutant conditions. Overall design: We isolated replication intermediates to purify short nascent strands of increasing size (Fractions 3, 4 and 5+6+7) from two developmental stages of Arabidopsis seedlings (4 and 10 day-old). For each developmental stage we processed three independent biological replicates and two genomic controls. A total of 20 samples were sequenced. We also did RNA-seq of 4 day-old seedlings in duplicate (2 samples).