Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA108275 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:SPO11-promoted DNA double-strand breaks (DSBs) formation is a crucial step for meiotic recombination, and it is indispensable to detect the broken DNA ends accurately for dissecting the molecular mechanisms behind. Here, we report a novel technique, named DEtail-seq (DNA End tailing followed by sequencing), that can directly and quantitatively capture the meiotic DSB 3’ overhang hotspots at single-nucleotide resolution.
2023-01-08 | GSE154227 | GEO
Project description:Human DNA replication relies on the activation of thousands of origins distributed along the genome. Their organization and the functional significance of their distribution remains unknown. To map large number of origins in human cells, we have localized the distribution of short nascent DNA using a high-resolution DNA tiling array platform covering 33.9Mb. Results with three different cell lines reveal that origins are very closely spaced (average interval 3-5kb), and that their positions are largely conserved among the cell lines studied. Origins are non-randomly distributed, being preferentially enriched at the 5’-end of expressed genes and at evolutionary intergenic sequences. In MCF7 cells, a strong correlation is also found between origin positioning and histone H3K4me3 and of PolII binding to chromatin. This study provides a large scale view of the organization of DNA replication origins in human chromosomes and suggests a link between this distribution and underlying chromatin features related to chromosome structure, and gene expression Keywords: nascent strand DNA, histone, Pol-II ChIP-chip. To map initiation sites for DNA replication and the position of both H3K4Me3 and Pol-II chromatin binding sites in human cell lines on a custom made high density tiling DNA microarray covering 33.9 Mb of the human genome.
2011-05-13 | E-GEOD-10917 | biostudies-arrayexpress
Project description:Genome-wide mapping of human DNA-replication origins: levels of transcription at Orc1 sites regulate origin selection and replication timing
| PRJNA162295 | ENA
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:Recurrent DNA break clusters (RDCs) are replication and transcription collision hotspots. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unraveled the replication fork architecture dictating RDC location and orientation. Most RDC occurs at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSB) while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bounded RNA revealed transient DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping nascent RNA and RNA polymerase activity revealed that head-to-head interactions between replication and transcription machinery slow down DNA replication, resulting in 60% DSB contribution to the head-on as compared to 60% for co-directional . Our findings revealed TTR as a novel fragile class and highlighted how the linear interaction between transcription and replication impacts genome stability.
2024-03-18 | GSE254765 | GEO
Project description:Mapping origins of replication has been challenging in higher eukaryotes. We have developed a rapid, genome-wide method to map origins in asynchronous human cells by combining the nascent strand abundance assay with a highly-tiled microarray platform, and we validated the technique by two independent assays. We applied this method to analyze the enrichment of nascent DNA in three 50 kb regions containing known origins of replication in the MYC, LMNB2, and HBB genes, a 200 kb region containing the rare fragile site, FRAXA, and a 1075 kb region on chromosome 22, and detected most of the known origins, as well as 28 new origins. Surprisingly, the 28 new origins were small in size, and predominantly located within genes. Our study also revealed a strong correlation between origin replication timing and chromatin acetylation. Keywords: origin mapping, nascent strand DNA, histone acetylaction mapping, ChIP-chip
2007-05-26 | GSE7889 | GEO
Project description:DNA replication of eukaryotic chromosomes initiates at a number of discrete loci, called replication origins. Distribution and regulation of origins are important for complete duplication of the genome. Here, we determined locations of Orc1 and Mcm6, components of pre-replicative complex (pre-RC), on whole genome of Schizosaccharomyces pombe using a high-resolution tiling array. Pre-RC sites were identified in 460 intergenic regions, where Orc1 and Mcm6 colocalized. By mapping of 5-bromo-2’-deoxyuridine (BrdU)-incorporated DNA in the presence of hydroxyurea (HU), 307 pre-RC sites were identified as early-firing origins. In contrast, 153 pre-RC sites without BrdU incorporation were considered to be late and/or inefficient origins. Early and late origins tend to distribute separately in large chromosome regions. Inactivation of replication checkpoint by deletion of Cds1 resulted in BrdU incorporation with HU specifically at the late origins. An origin-exchange experiment showed that replication timing was not intrinsic to origin but dependent on its surrounding region. Interestingly, pericentromeric heterochromatin and the silent mating type locus replicated in the presence of HU, while the inner centromere or subtelomeric heterochromatin did not. Notably, MCM did not bind to inner centromeres where ORC was located. Thus, replication is differentially regulated in chromosome domains. Keywords: ChIP-chip analysis
2007-03-05 | GSE6523 | GEO
Project description:Map the origins of DNA replication in human cells at 7 common fragile sites and their flanking non-fragile sequences as well as a 200kb containing the rare fragile site FRAXA, and a 1,075kb non-fragile region on chr22 . The origins were mapped in untreated cells, as well as, in cells treated with aphidicolin (APH), trichostatin A (TSA), or APH plus TSA. The origin mapping experiment is based on the fact that during S phase, short newly replicated DNA fragments (300bp-1kb) are generated only at the origins of replication. By combining the nascent strand assay with a tiled microarray platform, we have previoulsy developed a rapid, non-PCR based, high-throughput approach to map active origins in asynchronous human cells (Lucas et al., 2007, AC 17668008).
2010-02-27 | E-TABM-348 | biostudies-arrayexpress
Project description:High Resolution Mapping of DNA Copy Alterations in Human Chromosome 22 Using High Density Tiling Oligonucleotide Arrays
| PRJNA94897 | ENA
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