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The spatio-temporal program of DNA replication is driven by specific epigenetic signatures in human cells

ABSTRACT: We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA replication origins in K562 mammalian cells. We have optimized a specific method of peak detection adapted to the signal produced by the sequencing of short nascent strands (SNS) that are specific of replication initiation, with the aim to have both a good sensitivity and specificity. We demonstrated the existence of the spatiao-temporal program of DNA replication driven by a specific epigenetic signature.

ORGANISM(S): Homo sapiens

PROVIDER: GSE46189 | GEO | 2014/05/01

SECONDARY ACCESSION(S): PRJNA197531

REPOSITORIES: GEO

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The spatio-temporal program of DNA replication is driven by specific epigenetic signatures in human cells

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA replication origins in K562 mammalian cells. We have optimized a specific method of peak detection adapted to the signal produced by the sequencing of short nascent strands (SNS) that are specific of replication initiation, with the aim to have both a good sensitivity and specificity. We demonstrated the existence of the spatiao-temporal program of DNA replication driven by a specific epigenetic signature. K562 human cells; five samples subjected to SNS-Seq.

2014-05-01 | E-GEOD-46189 | biostudies-arrayexpress

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High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

Project description:At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, which genetic and chromatin features define metazoan replication start sites remains largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and show their ability to transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence specificity, mark and predict replication origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship between DNA topology, chromatin, transcription and replication initiation across metazoa. Our dataset consists of SNS-Seq profiles in Drosophila S2 and Bg3 cells. Small nascent leading strands (SNS) have been purified with an enhanced sensitivity SNS purification protocol. For standard SNS-Seq experiments (from pooled gradient fractions, denoted as "pool"), SNS were purified from two biological replicates. For single-fraction SNS-Seq experiments, two libraries were prepared for each fraction. The genomic coordinates of S2 and Bg3 replication origins are also provided.

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Project description:Here, we precisely determined MCM7 binding sites inHeLa cells by ChIP-Seq, classified them into firing and dormant replication origins using SNS data deposited, and analyzed their association with various chromatin signatures.

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Study of RepID/PHIP in DNA Replication inhitiation in Mammalian Cells

Project description:Mammalian chromosome replication starts from distinct sites, but the principles governing initiation site selection are unclear because proteins essential for DNA replication do not exhibit sequence-specific DNA binding. We identified a replication initiation determinant (RepID) protein that binds a subset of replication initiation sites. A large fraction of RepID binding sites share a common G-rich motif and exhibit elevated replication initiation. RepID is required for initiation of DNA replication from Rep-ID bound replication origins, including the origin at the human beta-globin (HBB) locus. At HBB, RepID is involved in an interaction between the replication origin (Rep-P) and the locus control region. RepID depleted murine embryonic fibroblasts exhibit abnormal replication fork progression and fewer replication initiation events. These observations are consistent with a model suggesting that RepID facilitates replication initiation at a distinct group of human replication origins. Nascent strands were purified with the lambda exonuclease methods from HCT116 cells and sequenced. Chromatin from unsyncrhonized untreated cultures of U2OS cells was subjected to ChIP-Seq with antibody directed against RepID/PHIP

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