ArticleGenome biology2012
Genome-wide identification and characterization of replication origins by deep sequencing.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 99 citations in OpenAlex.
- Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.Science (New York, N.Y.) · 2015Trial
- Stranded short nascent strand sequencing reveals the topology of DNA replication origins ineLife · 2026Article
- Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts.Microbial cell (Graz, Austria) · 2024Article
- CDMAP/CDVIS: context-dependent mutation analysis package and visualization software.G3 (Bethesda, Md.) · 2023Article
- Origins of DNA replication in eukaryotes.Molecular cell · 2023Review
- Article
- Ribonucleotide Incorporation by Eukaryotic B-Family Replicases and Its Implications for Genome Stability.Annual review of biochemistry · 2022Review
- Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication.Molecular cell · 2021Article
- Ribonucleotide incorporation into DNA during DNA replication and its consequences.Critical reviews in biochemistry and molecular biology · 2021Review
- Bioinformatical dissection of fission yeast DNA replication origins.Open biology · 2020Article
- Article
- DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family.Nature protocols · 2020Article
- Article
- Control of DNA replication timing in the 3D genome.Nature reviews. Molecular cell biology · 2019Review
- Roles for DNA polymerase δ in initiating and terminating leading strand DNA replication.Nature communications · 2019Article
- Involvement of G-quadruplex regions in mammalian replication origin activity.Nature communications · 2019Article
- Dynamics of DNA replication in a eukaryotic cell.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Autonomously Replicating Linear Plasmids That Facilitate the Analysis of Replication Origin Function inmSphere · 2019Article
- The evolution of the temporal program of genome replication.Nature communications · 2018Article
- PomBase: The Scientific Resource for Fission Yeast.Methods in molecular biology (Clifton, N.J.) · 2018Review
Corrections and comments
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Authors and funding
16 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood.
resultsWe have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions.
conclusionsThe sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.