ArticleScience (New York, N.Y.)2009
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.
Article in Science (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Convergent Evolution and the Epigenome.Epigenomes · 2025Review
- The topography of nullomer-emerging mutations and their relevance to human disease.Computational and structural biotechnology journal · 2025Article
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- Predicting regional somatic mutation rates using DNA motifs.PLoS computational biology · 2023Article
- Chromatin structure influences rate and spectrum of spontaneous mutations inGenome research · 2023Article
- The Adaptability of Chromosomal Instability in Cancer Therapy and Resistance.International journal of molecular sciences · 2022Review
- Nucleosomes effectively shield DNA from radiation damage in living cells.Nucleic acids research · 2020Article
- Article
- Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome.Nature communications · 2020Article
- A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.PLoS computational biology · 2018Article
- Human exonization through differential nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts.Epigenetics & chromatin · 2017Article
- Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum.PLoS genetics · 2017Article
- Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.Nucleic acids research · 2016Article
- Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome.Genome research · 2016Article
- Preferential Protection of Genetic Fidelity within Open Chromatin by the Mismatch Repair Machinery.The Journal of biological chemistry · 2016Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- Altered primary chromatin structures and their implications in cancer development.Cellular oncology (Dordrecht, Netherlands) · 2016Review
- The topography of mutational processes in breast cancer genomes.Nature communications · 2016Article
23 more citing papers are in PubMed but not listed here.
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18 authors.
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Abstract
Might DNA sequence variation reflect germline genetic activity and underlying chromatin structure? We investigated this question using medaka (Japanese killifish, Oryzias latipes), by comparing the genomic sequences of two strains (Hd-rR and HNI) and by mapping approximately 37.3 million nucleosome cores from Hd-rR blastulae and 11,654 representative transcription start sites from six embryonic stages. We observed a distinctive approximately 200-base pair (bp) periodic pattern of genetic variation downstream of transcription start sites; the rate of insertions and deletions longer than 1 bp peaked at positions of approximately +200, +400, and +600 bp, whereas the point mutation rate showed corresponding valleys. This approximately 200-bp periodicity was correlated with the chromatin structure, with nucleosome occupancy minimized at positions 0, +200, +400, and +600 bp. These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute to molding the DNA sequence on an evolutionary time scale.
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