TY - JOUR
T1 - Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin
AU - Vergara, Zaida
AU - Sequeira-Mendes, Joana
AU - Morata, Jordi
AU - Peiró, Ramón
AU - Hénaff, Elizabeth
AU - Costas, Celina
AU - Casacuberta, Josep M.
AU - Gutierrez, Crisanto
N1 - Funding Information:
We thank the Confocal Microscopy and Flow Cytometry Services of CBMSO and V. Mora-Gil for technical assistance. We also thank M. Bernadó of CRAG’s genomics facility for assistance with statistical analyses. We thank E. Martinez-Salas for comments on the manuscript. Z.V. has been recipient of a FPI Predoctoral Fellowship from MINECO.
Publisher Copyright:
© The Author(s) 2017.
PY - 2017/8/21
Y1 - 2017/8/21
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85031844541&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85031844541&partnerID=8YFLogxK
U2 - 10.1093/nar/gkx524
DO - 10.1093/nar/gkx524
M3 - Article
C2 - 28605523
AN - SCOPUS:85031844541
SN - 0305-1048
VL - 45
SP - 8358
EP - 8368
JO - Nucleic acids research
JF - Nucleic acids research
IS - 14
ER -