Mapping of human DNA replication origins
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB12207 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1195480.fastq.gz | Fastqsanger.gz | |||
| ERR1195481.fastq.gz | Fastqsanger.gz | |||
| ERR1195479.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We describe a modification of initiation site sequencing (ini-seq, Langley et al., NAR 2016) in which density gradient centrifugation separates ‘heavy’ replicated DNA containing BrdU from DNA containing only ‘light’ dTTP before sequencing. This approach allows us to assign a replication initiation efficiency score to each of the 23905 origins identified. We also performed Short Nascent Strand sequencing (SNS-seq), an established method to map replication origins, in the same cell line as in Ini-seq2 for comparison.
2022-06-15 | GSE186675 | GEO
Project description: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 5M-bM-^@M-^Y half of genes, enriched in histone H2A.Z, H3K4me2/3 and acetylated 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. This SuperSeries is composed of the following subset Series: GSE21781: Mapping origins of replication in Arabidopsis thaliana: Examination of BrdU labelled DNA and unlabelled DNA in one cell type GSE21827: Mapping origins of replication in Arabidopsis thaliana: H3K4ac ChIP vs. unmodified H3 ChIP Refer to individual Series
2011-02-06 | E-GEOD-21828 | biostudies-arrayexpress
Project description: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 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. This SuperSeries is composed of the SubSeries listed below.
2011-02-06 | GSE21828 | GEO
Project description: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 5M-bM-^@M-^Y 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. H4K5ac ChIP vs. unmodified H3 ChIP. Our study utilizes the following datasets in addition to the data we generated: H3K4me1: GSM343141 H3K4me2: GSM343143 H3K4me3: GSM343144 H3K9me2: GSM310840 H2AZ: GSM307373
2011-11-06 | E-GEOD-21827 | biostudies-arrayexpress
Project description: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.
2011-11-06 | GSE21827 | GEO
Project description:Because of the lack of information, regulation of DNA replication initiation in mammals is still poorly understood. In order to identify general rules, we have mapped replication origins along 1% of the human genome in HeLa cells. We found large gene-poor regions lacking origin and G+C rich regions containing clusters of closely spaced origins. Half of the 283 origins mapped are within or near CpG islands. The connection with gene expression is further reinforced by the observation that most origins overlap with DNAseI hypersensitive sites found at transcriptional regulatory elements. We show, however, that this association is independent of chromatin structure and transcriptional activity. Replication timing analyses coupled to our origin mapping demonstrate that origin dense regions and isolated origins are replicated at every moment in S phase. All together, our data suggest that a relatively strict origin-timing programme regulates DNA replication of the human genome. Keywords: Nascent strands, ENCODE project, HeLAS3 cells, SNS-Chip
2008-10-22 | GSE10217 | GEO
Project description: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
2011-11-06 | E-GEOD-21781 | biostudies-arrayexpress
Project description:Because of the lack of information, regulation of DNA replication initiation in mammals is still poorly understood. In order to identify general rules, we have mapped replication origins along 1% of the human genome in HeLa cells. We found large gene-poor regions lacking origin and G+C rich regions containing clusters of closely spaced origins. Half of the 283 origins mapped are within or near CpG islands. The connection with gene expression is further reinforced by the observation that most origins overlap with DNAseI hypersensitive sites found at transcriptional regulatory elements. We show, however, that this association is independent of chromatin structure and transcriptional activity. Replication timing analyses coupled to our origin mapping demonstrate that origin dense regions and isolated origins are replicated at every moment in S phase. All together, our data suggest that a relatively strict origin-timing programme regulates DNA replication of the human genome. Keywords: Nascent strands, ENCODE project, HeLAS3 cells, SNS-Chip Four independent preparations of Short Nascent Strands (SNS) were performed. In order to have enough material for microarray hybridisation, we coupled the stringent preparation of SNS with the TLAD method, a technique of linear amplification that can generate several µg of amplified material from 10-20 ng of DNA (Liu et al., 2003).Two were amplified by TLAD (experiments A and B) and hybridized on DNA microarrays, and the other two (experiments C and D) were used for the validation by real-time quantitative PCR (qPCR) of results obtained on micro-arrays. We performed also a gDNA/gDNA hybridization where gDNA are also amplified by TLAD to order to do a control.
2010-05-18 | E-GEOD-10217 | biostudies-arrayexpress
Project description:The initiation of DNA synthesis in metazoans is restricted to a group of baseline replication origins, whereas other (dormant) origins do not initiate replication despite recruiting apparently indistinguishable pre-replication complexes. Dormant origins are activated as backups when DNA synthesis stalls. We report that dormant origins selectively bind CDK-phosphorylated RecQL4 (pRecQL4), a helicase mutated in Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. In unperturbed cells, pRecQL4 restricts replication initiation to baseline origins by preventing dormant origins from binding the essential initiation factor MTBP. When cells encounter replication stress, pRecQL4 first promotes the dissociation of MTBP from chromatin, and then enables its redistribution to both baseline and dormant origins, facilitating compensatory initiation to complete genome duplication. Thus, MTBP-pRecQL4 interactions modulate replication origin choice and facilitate recovery from replication stress.
2025-04-06 | GSE276856 | GEO
Project description: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.
2011-11-06 | GSE21781 | GEO