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Series GSE21781 Query DataSets for GSE21781
Status Public on Nov 06, 2011
Title Mapping origins of replication in Arabidopsis thaliana: Examination of BrdU labeled DNA and unlabeled DNA in one cell type
Organism Arabidopsis thaliana
Experiment type Other
Summary 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.
 
Overall design Examination of BrdU labelled DNA and unlabelled DNA in one cell type
 
Contributor(s) Stroud H
Citation(s) 21297636
Submission date May 11, 2010
Last update date May 15, 2019
Contact name Hume Stroud
Organization name UT Southwestern
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platforms (1)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
Samples (4)
GSM542644 BrdU labelled DNA rep1
GSM542645 Unlabelled DNA rep1
GSM588602 BrdU labelled DNA rep2
This SubSeries is part of SuperSeries:
GSE21828 Mapping origins of replication in Arabidopsis thaliana
Relations
SRA SRP002528
BioProject PRJNA129357

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21781_RAW.tar 174.5 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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