Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin

Abstract

Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a highresolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with retrotransposons is determined by their transposition mechanism based on transcription, and a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin and of the entire genome.

Silenced retrotransposons are major rasiRNAs targets in Arabidopsis galls induced by Meloidogyne javanica

“…Interestingly, CG‐rich heterochromatic states have recently been shown to be determinant features for the localization of DNA replication origins (ORIs) in heterochromatin. In particular, GYPSY retrotransposon elements co‐localized with ORIs at pericentromeric gene‐poor regions in Arabidopsis (Vergara et al., ). dGall‐rasiRNAs at 3 dpi are mainly accumulated at retrotransposon superfamilies, preferentially GYPSY superfamilies at pericentromeric regions, and expression analysis indicated that key members of several retrotransposon families, such as ATHILA2 , were repressed (Fig.…”

Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin

“…Studies. An earlier paper and follow up studies from the Gutierrez lab using Arabidopsis Ler-0 suspension cells defined as origins a set of loci that are GC-rich sequences associated with the 5' ends of genes and enriched for the acetylated histone H4K5ac (Costas et al, 2011;Xing et al, 2014;Sequeira-Mendes and Gutierrez, 2015;Vergara et al, 2017;Sequeira-Mendes et al, 2019). To compare our IRs with the loci defined in these studies, we plotted replication signal enrichment from our data around the loci defined by Costas et al and Vergara et al Neither set of loci defined by the Gutierrez group showed local increases in replication signal across a ±15 kb window, in spite of the fact that their loci were identified using BrdU, a thymidine analog similar to EdU (Supplemental Fig.…”

“…S2A). The Gutierrez group used a single BrdU dataset, in which they identified either 1,534 or 3,230 putative origins depending on the peak calling algorithm used (MACS and MACS2, respectively) (Costas et al, 2011;Vergara et al, 2017). The same group reported a high level of variability between biological replicates when using the SNS assay to identify putative origins in Arabidopsis Col-0 seedlings (Sequeira-Mendes et al, 2019).…”

“…Previous efforts to map origins in Arabidopsis, using SNS analysis as a validation method or as the primary assay (Costas et al, 2011;Vergara et al, 2017;Sequeira-Mendes et al, 2019), suffer the same low reproducibility common to SNS experiments in other systems. In addition, the first origin study in Arabidopsis subjected cells to sucrose starvation and hydroxyurea treatment, both of which can alter origin usage (Taylor, 1977;Ge et al, 2007;Gilbert, 2007).…”

Correlated evolution of large DNA fragments in the 3D genome of Arabidopsis thaliana

“…Genome-wide feature data processing and regression analysis and averaged for each window. The coverage of replication origins was calculated using data from Vergara et al (2017). The replication timing of three categories (i.e., early, mid, and late)…”