ArticleNature communications2013
DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes.
Article in Nature communications, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Determinants of mutation susceptibility along the genome are largely invariant across human tissues.Genome biology · 2026Article
- Induced DNA double strand breaks by genotoxic drugs occur at active transcription H3K36 tri-methylation sites.Communications biology · 2026Article
- Therapy-associated mutagenesis at CTCF binding sites is shaped by chromatin context and DNA repair capacity.bioRxiv : the preprint server for biology · 2026Article
- Interplay of replication timing, DNA repair, and translesion synthesis in UV mutagenesis in yeast.Nucleus (Austin, Tex.) · 2025Article
- Single cell multiomics approach to analyze replication timing and gene expression in mouse preimplantation embryos.Communications biology · 2025Article
- Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.Nature communications · 2025Article
- Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution.Nature communications · 2024Article
- Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers.Nature cancer · 2024Article
- Predicting regional somatic mutation rates using DNA motifs.PLoS computational biology · 2023Article
- Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin.PLoS computational biology · 2022Article
- Review
- Mutational Signatures of Replication Timing and Epigenetic Modification Persist through the Global Divergence of Mutation Spectra across the Great Ape Phylogeny.Genome biology and evolution · 2022Article
- Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions.Frontiers in cell and developmental biology · 2022Review
- Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes.NAR cancer · 2021Article
- Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas.Leukemia · 2021Article
- Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship.International journal of molecular sciences · 2021Review
- GPSeq reveals the radial organization of chromatin in the cell nucleus.Nature biotechnology · 2020Article
- Mutational signature SBS8 predominantly arises due to late replication errors in cancer.Communications biology · 2020Article
- Mechanisms of UV-induced mutations and skin cancer.Genome instability & disease · 2020Article
- Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Single-nucleotide substitutions are a defining characteristic of cancer genomes. Many single-nucleotide substitutions in cancer genomes arise because of errors in DNA replication, which is spatio-temporally stratified. Here we propose that DNA replication patterns help shape the mutational landscapes of normal and cancer genomes. Using data on five fully sequenced cancer types and two personal genomes, we determined that the frequency of intergenic single-nucleotide substitution is significantly higher in late DNA replication timing regions, even after controlling for a number of genomic features. Furthermore, some substitution signatures are more frequent in certain DNA replication timing zones. Finally, integrating data on higher-order nuclear organization, we found that genomic regions in close spatial proximity to late-replicating domains display similar mutation spectra as the late-replicating regions themselves. These data suggest that DNA replication timing together with higher-order genomic organization contribute to the patterns of single-nucleotide substitution in normal and cancer genomes.
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