ArticleGenome research2011
Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
42 citing papers in PubMed, 66 citations in OpenAlex.
- CG-Based Stratification of 8-mers Highlights Functional Roles and Phylogenetic Divergence Markers.International journal of molecular sciences · 2025Article
- Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection.PLoS biology · 2022Article
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure.Briefings in bioinformatics · 2021Article
- Review
- Somatic mutations in colorectal cancer are associated with the epigenetic modifications.Journal of cellular and molecular medicine · 2020Article
- Epigenetics and genome stability.Mammalian genome : official journal of the International Mammalian Genome Society · 2020Review
- Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome.Nature communications · 2020Article
- EvoChromo: towards a synthesis of chromatin biology and evolution.Development (Cambridge, England) · 2019Review
- Human exonization through differential nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- Nucleosomal organization and DNA base composition patterns.Nucleus (Austin, Tex.) · 2017Review
- Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder.Nature neuroscience · 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
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- Article
- Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects.G3 (Bethesda, Md.) · 2015Article
- Genomic approaches to DNA repair and mutagenesis.DNA repair · 2015Review
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
In this study we investigated the strengths and modes of selection associated with nucleosome positioning in the human lineage through the comparison of interspecies and intraspecies rates of divergence. We identify significant evidence for both positive and negative selection linked to human nucleosome positioning for the first time, implicating a widespread and important role for DNA sequence in the location of well-positioned nucleosomes. Selection appears to be acting on particular base substitutions to maintain optimum GC compositions in core and linker regions, with, e.g., unexpectedly elevated rates of C→T substitutions during recent human evolution at linker regions 60-90 bp from the nucleosome dyad but significant depletion of the same substitutions within nucleosome core regions. These patterns are strikingly consistent with the known relationships between genomic sequence composition and nucleosome assembly. By stratifying nucleosomes according to the GC content of their genomic neighborhood, we also show that the strength and direction of selection detected is dictated by local GC content. Intriguingly these signatures of selection are not restricted to nucleosomes in close proximity to exons, suggesting the correct positioning of nucleosomes is not only important in and around coding regions. This analysis provides strong evidence that the genomic sequences associated with nucleosomes are not evolving neutrally, and suggests that underlying DNA sequence is an important factor in nucleosome positioning. Recent signatures of selection linked to genomic features as ubiquitous as the nucleosome have important implications for human genome evolution and disease.
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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.