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PMID: 21297636 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks.

Nature structural & molecular biology ·Vol. 18 ·No. 3 ·2011-03-00 ·Pages 395-400

Costas C, de la Paz Sanchez M, Stroud H, Yu Y, Oliveros JC, Feng S, Benguria A, López-Vidriero I, Zhang X, Solano R, Jacobsen SE, Gutierrez C

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.

MeSH Terms
Arabidopsis/genetics,metabolism Arabidopsis Proteins/genetics,metabolism Cell Cycle Proteins/metabolism Chromatin/metabolism Chromosome Mapping DNA Replication DNA, Plant/genetics Epigenomics Histones/genetics Origin Recognition Complex/metabolism Protein Binding Replication Origin
Chemicals
Arabidopsis Proteins CDC6 protein, Arabidopsis Cell Cycle Proteins Chromatin DNA, Plant H2A.Z protein, Arabidopsis Histones Origin Recognition Complex
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Costas Celina
Consejo Superior de Investigaciones Científicas -Universidad autónoma de Madrid, Madrid, Spain.
de la Paz Sanchez Maria
Stroud Hume
Yu Yanchun
Oliveros Juan Carlos
Feng Suhua
Benguria Alberto
López-Vidriero Irene
Zhang Xiaoyu
Solano Roberto
Jacobsen Steven E
Gutierrez Crisanto
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Article Info
Journal
Nature structural & molecular biology
Abbr.
Nat Struct Mol Biol
ISSN
1545-9985
DOI
10.1038/nsmb.1988
Published
2011-03-00
Epub
2011-00-06
Pages
395-400
Language
English
Region
United States
NLM ID
101186374
PMCID
PMC3079358
Subset
IM
Grants
NIGMS NIH HHS · R37 GM060398 · United States
NIGMS NIH HHS · R37 GM060398-10 · United States
Howard Hughes Medical Institute · United States
NIGMS NIH HHS · R01 GM060398 · United States
NIGMS NIH HHS · GM60398 · United States
External Links
PubMed source DOI: 10.1038/nsmb.1988 PMC Full Text View journal details
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