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

Zaida Vergara, Joana Sequeira-Mendes, Jordi Morata, Ramón Peiró, Elizabeth Hénaff, Celina Costas, Josep M. Casacuberta, Crisanto Gutierrez

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)8358-8368
Number of pages11
JournalNucleic acids research
Volume45
Issue number14
DOIs
StatePublished - 2017

ASJC Scopus subject areas

  • Genetics

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    Vergara, Z., Sequeira-Mendes, J., Morata, J., Peiró, R., Hénaff, E., Costas, C., Casacuberta, J. M., & Gutierrez, C. (2017). Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. Nucleic acids research, 45(14), 8358-8368. https://doi.org/10.1093/nar/gkx524