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ABSTRACT:
PROVIDER: PRJEB50302 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We mapped Tetrahymena macronuclear replication origins on a genome-wide scale using nanopore sequencing. Nanopore sequencing quantifies individual BrdU incorporated replication intermediates on individual DNA molecules.
2025-08-08 | GSE210741 | GEO
Project description:The replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We now report a sequencing method for the measurement of replication fork movement on single molecules by Detecting Nucleotide Analogue signal currents on extremely long nanopore traces (D‑NAscent). Using this method, we detect BrdU incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse labelling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kb, to generate the first whole genome single-molecule map of DNA replication dynamics and discover a new class of low frequency stochastic origins in budding yeast.
2019-03-29 | GSE121941 | GEO
Project description:The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing. Increases in BrdU incorporation allow us to measure DNA replication dynamics, including identification of replication initiation, fork direction and termination on individual nanopore sequencing reads. Importantly, initiation and termination events are identified on single-molecules with high resolution, throughout S-phase and across the human genome. We find a significant enrichment of initiation sites within the broad initiation zones identified by population level studies. However, these focused sites only account for ~20% of all identified replication initiation events. Most initiation events are dispersed throughout the genome and are missed by cell population approaches. This indicates that most initiation occurs at sites that, individually, are rarely used. These dispersed initiation sites contrast with the focused sites identified by population studies, in that they do not show a strong relationship to transcription or a particular epigenetic signature. Therefore, single-molecule sequencing enables unbiased detection and characterisation of DNA replication initiation events, including the numerous dispersed initiation events that replicate most of the human genome.
2025-04-03 | GSE265956 | GEO
Project description:In order to analyze the relationship between the replication fork direction and the repair products at a specific genomic sites, we performed nascent strand sequencing of U2OS cells to mapping strong origins in genome, which can indicate the replication fork direction of a specific site adjacent to the origin.
2025-11-18 | GSE309838 | GEO
Project description:We mapped Tetrahymena macronuclear replication origins on a genome-wide scale using Okazaki fragments sequencing (OK-seq). OK-seq permits a high-resolution, quantitative analysis of replication fork initiation on a genome-wide scale that is dependent on the depth of coverage within a population of molecules. Replication initiation sites of the TXR1 (Histone H3 K27 monomethyltranferase) deletion strain were also studied compare to wild type using OK-seq.
2025-07-31 | GSE210487 | GEO
Project description:Genome-wide replication fork directionality measured by strand-specific sequencing of Okazaki fragments in chicken lymphoma cells (DT40).
2022-02-18 | GSE196761 | GEO
Project description:Every nucleosome across the genome must be disrupted and reformed when the replication fork passes, but how chromatin organization is re-established following replication is unknown. To address this problem, we have developed Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq) to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution. We find that the characteristic chromatin landscape at Drosophila promoters and enhancers is lost upon replication. The most conspicuous changes are at promoters that have high levels of RNA polymerase II (RNAPII) stalling and DNA accessibility and show specific enrichment for the BRM remodeler. Enhancer chromatin is also disrupted during replication, suggesting a role for transcription factor (TF) competition in nucleosome re-establishment. Thus, the characteristic nucleosome landscape emerges from a uniformly packaged genome by the action of TFs, RNAPII and remodelers minutes after replication fork passage.
2016-04-07 | GSE76120 | GEO
Project description:Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing
| PRJEB57572 | ENA
Project description:Although Poly(ADP-ribose)-polymerases (PARPs) are key regulators of genome stability, how site-specific ADP-ribosylation regulates DNA repair is unclear. Here, we describe a novel role for PARP1 and PARP2 in regulating Rad52-dependent replication fork repair to maintain cell viability when HR is dysfunctional, suppress replication-associated DNA damage, and maintain genome stability. Mechanistically, Mre11 is required for induction of PARP activity in response to replication stress that in turn promotes break-induced replication (BIR) through assembly of Rad52 at stalled/damaged replication forks. Further, by mapping ADP-ribosylation sites induced upon replication stress, we identify that PolD3 is a target for PARP1/PARP2 and importantly, that its site-specific ADP-ribosylation is required for BIR activity, replication fork recovery and genome stability. Overall, these data identify a critical role for Mre11-dependent PARP activation and site-specific ADP-ribosylation in regulating BIR to maintain genome integrity during DNA synthesis.
2023-10-24 | PXD035661 | Pride
Project description:Methylation based plasmid binning using nanopore sequencing
| PRJEB54092 | ENA