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TranscriptomicsTranscription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells
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 an...
ORGANISM(S): Mus musculus 
2010-05-22 | E-GEOD-15082 | biostudies-arrayexpress
GenomicsUnraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs
Short nascent strands purification coupled to next-generation sequencing allowed us to identify replication origins on human genome in an extensive way, by mapping replication origins in 4 different cell types, IMR-90 fibroblasts, hESC H9 cells, iPSC Th Cl-4 cells and HeLa cells. We demonstrated the...
ORGANISM(S): Homo sapiens 
2012-07-01 | E-GEOD-37757 | biostudies-arrayexpress
TranscriptomicsGenome-wide Profiling of DNA Replication Timing in pombe.
DNA replication is initiated at multiple sites or origins enriched with AT-rich sequences at various times during the S-phase. While current studies of genome-wide DNA replication profiles have focused on the timing of replication and the location of origins, the efficiency of replication/firing at...
ORGANISM(S): Schizosaccharomyces pombe 
2007-08-14 | E-GEOD-6977 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of yeast strains in which Hsk1-Dfp1 has been tethered near a replication origin
Transcription profiling of strains in which Hsk1-Dfp1 has been tethered near a replication origin.
ORGANISM(S): Schizosaccharomyces pombe 
2008-09-25 | E-MEXP-1811 | biostudies-arrayexpress
GenomicsGenome-wide mapping of human DNA-replication origins: levels of transcription at Orc1 sites regulate origin selection and replication timing
We report the genome-wide mapping of Orc1 binding-sites in mammals and their validation as active DNA-replication origins (ORIs). Orc1 sites are universally associated with transcription start sites (TSSs) of coding or non-coding RNAs. Transcription levels at the Orc1 sites directly correlate with r...
ORGANISM(S): Homo sapiens 
2012-09-18 | E-GEOD-37583 | biostudies-arrayexpress
TranscriptomicsSingle-Stranded Annealing Induced by Re-Initiation of Replication Origins Provides a Novel and Efficient Mechanism for Generating Copy Number Expansion via Non-Allelic Homologous Recombination.
Copy number expansions such as amplifications and duplications contribute to human phenotypic variation, promote molecular diversification during evolution, and drive the initiation and/or progression of various cancers. The mechanisms underlying these copy number changes are still incompletely unde...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-04 | E-GEOD-41259 | biostudies-arrayexpress
TranscriptomicsComparative genomic hybridization of S. pombe co-overexpressing DNA synthesis initiation factors cdc18 (cdc6) and cdt1 to investigate gene copy number increases
During S-phase of the eukaryotic cell cycle, controls exist to ensure that replication origins fire only once and become inactivated after traverse of a replication fork. Failure of these controls results in local amplification of the genome which can lead to gene copy increases important for both ...
ORGANISM(S): Schizosaccharomyces pombe 
2010-08-13 | E-MTAB-139 | biostudies-arrayexpress
GenomicsSingle molecule MATAC-seq reveals key determinants of DNA replication origin efficiency
Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency
PRJNA911675 | ENA
GenomicsDetermination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation
Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation
PRJNA775057 | ENA
TranscriptomicsQuantitative, genome-wide analysis of eukaryotic replication initiation and termination
Via the deep-sequencing of Okazaki fragments from Saccharomyces cerevisiae, we report the first comprehensive documentation of genome-wide replication directionality in any eukaryote; this permits the systematic analysis of both replication initiation and termination. We conduct a genome-wide analys...
ORGANISM(S): Saccharomyces cerevisiae 
2013-02-28 | E-GEOD-40696 | biostudies-arrayexpress
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