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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:Balancing replication fork progression and origin usage is essential to maintain genome stability, but measuring replication fork progression rates and origin usage throughout the genome has been challenging. Here, we use nanopore sequencing combined with DNAscent to measure replication fork progression together with origin and termination site usage with single-molecule precision throughout the Drosophila genome with nearly full genome coverage. We find that replication fork progression rates are not uniform throughout the genome. Rather, fork progression is slowest in euchromatin, and this is not correlated with active transcription. Replication origins are also influenced by chromatin, but the exact position of initiation is highly variable and are often several kilobases away from ORC binding sites. Termination sites lack any chromatin or sequence motifs and appear nearly random throughout the genome. By measuring DNA replication dynamics at near full genome coverage, our work reveals key principles of metazoan replication dynamics.
2026-03-24 | GSE309672 | 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:We profiled single-molecule DNA replication dynamics in human HCT116 cells to determine how WEE1 inhibition and stabilization of the origin-firing factor TRESLIN (TICRR) influence replication initiation, termination, and fork progression. We analyzed two engineered HCT116 lines expressing mClover-tagged TRESLIN from the endogenous locus: a wild-type TRESLIN allele and a stabilized ΔSBI TRESLIN mutant. Cells were treated with the WEE1 inhibitor MK-1775 (1 µM) or vehicle and sequentially pulse-labeled with EdU and BrdU, followed by a thymidine chase, to generate replication tracts for long-read nanopore sequencing. High–molecular weight genomic DNA was prepared and sequenced on an Oxford Nanopore PromethION platform, and reads were aligned to the human reference genome (hg38/GRCh38). Replication features (leftward/rightward forks, initiation events, and termination events) and tract lengths were inferred from EdU/BrdU segmentation using DNAscent forkSense, enabling quantification of fork directionality and fork rates across conditions. Associated preprint: bioRxiv [Preprint]. 2025 Jun 11;2025.06.10.657920. doi:10.1101/2025.06.10.657920.
2026-04-17 | GSE320256 | 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: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: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:Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing
| PRJEB57572 | ENA