Transcriptomics

Dataset Information

298

Mapping origins of replication in Arabidopsis thaliana: Examination of BrdU labeled DNA and unlabeled DNA in one cell type


ABSTRACT: Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. Here we have profiled origins in Arabidopsis thaliana by high-throughput sequencing of purified nascent DNA strands. We have identified 1543 replication origins, which were uniformly distributed across the Arabidopsis genome and enriched in binding signals of two replication initiation proteins, CDC6 and ORC1. We have also analyzed novel epigenome maps of various histone modifications and found links between origins and epigenetic signatures, which differ from or have not been reported for other eukaryotic systems. Arabidopsis origins tend to be embedded in G+C-rich regions within the 5’ half of genes, enriched in histone H2A.Z, H3K4me2/3 and acetylated H3 and H4, and depleted of H3K4me1 and H3K9me2. Our data establish the basis for the understanding of the epigenetic specification of origins of replication in Arabidopsis and have implications for the mechanisms of origin specification in other eukaryotes. Examination of BrdU labelled DNA and unlabelled DNA in one cell type

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Hume Stroud  

PROVIDER: E-GEOD-21781 | ArrayExpress | 2011-11-06

SECONDARY ACCESSION(S): GSE21781SRP002528PRJNA129357

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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

Costas Celina C   de la Paz Sanchez Maria M   Stroud Hume H   Yu Yanchun Y   Oliveros Juan Carlos JC   Feng Suhua S   Benguria Alberto A   López-Vidriero Irene I   Zhang Xiaoyu X   Solano Roberto R   Jacobsen Steven E SE   Gutierrez Crisanto C  

Nature structural & molecular biology 20110206 3


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)  ...[more]

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