title: Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks.
abstract: Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ~1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5' half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.
authors.affiliation: Consejo Superior de Investigaciones Científicas -Universidad autónoma de Madrid, Madrid, Spain.
authors.forename: Celina
authors.initials: C
authors.lastname: Costas
authors.forename: Maria
authors.initials: M
authors.lastname: de la Paz Sanchez
authors.forename: Hume
authors.initials: H
authors.lastname: Stroud
authors.forename: Yanchun
authors.initials: Y
authors.lastname: Yu
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Oliveros
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.forename: Alberto
authors.initials: A
authors.lastname: Benguria
authors.forename: Irene
authors.initials: I
authors.lastname: López-Vidriero
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.forename: Roberto
authors.initials: R
authors.lastname: Solano
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
authors.forename: Crisanto
authors.initials: C
authors.lastname: Gutierrez
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D002874:Chromosome Mapping; D004261:DNA Replication; D018744:DNA, Plant / Q000235:genetics*; D057890:Epigenomics; D006657:Histones / Q000235:genetics; D051738:Origin Recognition Complex / Q000378:metabolism; D011485:Protein Binding; D018741:Replication Origin
chemical_list: D029681:Arabidopsis Proteins; D018797:Cell Cycle Proteins; D002843:Chromatin; D018744:DNA, Plant; D006657:Histones; D051738:Origin Recognition Complex; C450459:CDC6 protein, Arabidopsis; C548103:AT1G52740 protein, Arabidopsis