E-GEOD-15082 - Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells

Status
Submitted on 3 March 2009, released on 22 May 2010, last updated on 4 May 2014
Organism
Mus musculus
Samples (8)
Array (1)
Protocols (9)
Description
Genomic mapping of DNA replication origins (ORIs) in mammals provides a powerful means for understanding the regulatory complexity of our genome. Here we combine a genome-wide approach to identify preferential sites of DNA replication initiation at 0.4% of the mouse genome with detailed molecular analysis at distinct classes of ORIs according to their location relative to the genes. Our study reveals that 85% of the replication initiation sites in mouse embryonic stem (ES) cells are associated with transcriptional units. Nearly half of the identified ORIs map at promoter regions and, interestingly, ORI density strongly correlates with promoter density, reflecting the coordinated organisation of replication and transcription in the mouse genome. Detailed analysis of ORI activity showed that CpG island promoter-ORIs are the most efficient ORIs in ES cells and both ORI specification and firing efficiency are maintained across cell types. Remarkably, the distribution of replication initiation sites at promoter-ORIs exactly parallels that of transcription start sites (TSS) suggesting a co-evolution of the regulatory regions driving replication and transcription. Moreover, we found that promoter-ORIs are significantly enriched in CAGE tags derived from early embryos relative to all promoters. This association implies that transcription initiation early in development sets the probability of ORI activation unveiling a new hallmark in ORI efficiency regulation in mammalian cells. Two biological replicates of lambda-exonuclease treated short nascent strands (100-600 or 300-800 nt in length) were co-hybridised with genomic DNA from the same cells to tiled genomic array covering 10.1 Mb of the mouse genome (Agilent Technologies)
Experiment type
other 
Contacts
Ramon Diaz-Uriarte <rdiaz02@gmail.com>, Anwyn Apedaile, Derek Huntley, Joana Sequeira-Mendes, María Gómez, Neil Brockdorff, Ramón Díaz-Uriarte
Citation
Transcription initiation activity sets replication origin efficiency in mammalian cells. Sequeira-Mendes J, Díaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, Gómez M.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-15082.idf.txt
Sample and data relationshipE-GEOD-15082.sdrf.txt
Raw data (1)E-GEOD-15082.raw.1.zip
Processed data (1)E-GEOD-15082.processed.1.zip
Array designA-GEOD-8246.adf.txt
R ExpressionSetE-GEOD-15082.eSet.r
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