ArticleNucleic acids research2016
The mutation spectrum in genomic late replication domains shapes mammalian GC content.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Mitochondrial genomic variation, evolutionary dynamics, and phylogeny of forest-associatedIMA fungus · 2026Article
- Telomere-to-telomere DNA replication timing profiling using single-molecule sequencing with Nanotiming.Nature communications · 2025Article
- Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution.Nature communications · 2024Article
- Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed).BMC bioinformatics · 2024Article
- The landscape of somatic mutations in lymphoblastoid cell lines.Cell genomics · 2023Article
- The effect of mutation subtypes on the allele frequency spectrum and population genetics inference.G3 (Bethesda, Md.) · 2023Article
- Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship.International journal of molecular sciences · 2021Review
- Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level.Frontiers in genetics · 2021Article
- Selection Shapes Synonymous Stop Codon Use in Mammals.Journal of molecular evolution · 2020Article
- Mutational signature SBS8 predominantly arises due to late replication errors in cancer.Communications biology · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development.Genome biology and evolution · 2019Article
- Germline DNA replication timing shapes mammalian genome composition.Nucleic acids research · 2018Article
- Replication timing and nuclear structure.Current opinion in cell biology · 2018Review
- Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans.PLoS genetics · 2018Article
- DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation.Genome research · 2017Article
- Perturbations in the Replication Program Contribute to Genomic Instability in Cancer.International journal of molecular sciences · 2017Review
- Order from clutter: selective interactions at mammalian replication origins.Nature reviews. Genetics · 2017Review
- Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement.Journal of visualized experiments : JoVE · 2017Article
- What Signatures Dominantly Associate with Gene Age?Genome biology and evolution · 2016Article
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Authors and funding
7 authors.
Funding
Abstract
Genome sequence compositions and epigenetic organizations are correlated extensively across multiple length scales. Replication dynamics, in particular, is highly correlated with GC content. We combine genome-wide time of replication (ToR) data, topological domains maps and detailed functional epigenetic annotations to study the correlations between replication timing and GC content at multiple scales. We find that the decrease in genomic GC content at large scale late replicating regions can be explained by mutation bias favoring A/T nucleotide, without selection or biased gene conversion. Quantification of the free dNTP pool during the cell cycle is consistent with a mechanism involving replication-coupled mutation spectrum that favors AT nucleotides at late S-phase. We suggest that mammalian GC content composition is shaped by independent forces, globally modulating mutation bias and locally selecting on functional element. Deconvoluting these forces and analyzing them on their native scales is important for proper characterization of complex genomic correlations.
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