The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
Transcription-associated mutational asymmetry in mammalian evolution
Abstract
Although mutation is commonly thought of as a random process, evolutionary studies show that different types of nucleotide substitution occur with widely varying rates that presumably reflect biases intrinsic to mutation and repair mechanisms. A strand asymmetry, the occurrence of particular substitution types at higher rates than their complementary types, that is associated with DNA replication has been found in bacteria and mitochondria. A strand asymmetry that is associated with transcription and attributable to higher rates of cytosine deamination on the coding strand has been observed in enterobacteria. Here, we describe a qualitatively different transcription-associated strand asymmetry in mammals, which may be a byproduct of transcription-coupled repair in germline cells. This mutational asymmetry has acted over long periods of time to produce a compositional asymmetry, an excess of G+T over A+C on the coding strand, in most genes. The mutational and compositional asymmetries can be used to detect the orientations and approximate extents of transcribed regions.
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“Private Asian and African TCC → T SNPs were found to exhibit the strand bias that is typical of A/C → G/T mutations (28), with the C → T change usually affecting the antisense strand and the G → A change usually affecting the sense strand.”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [28]
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1 retracted
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Self-citationThe DNA sequence of human chromosome 22
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Lobry, J. R. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025626 · Cited by 766
Transcription-Coupled Repair and Human Disease
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Cited by
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Detection of nonneutral substitution rates on mammalian phylogenies
Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., & Siepel, A. (2010) · Genome Research · doi:10.1101/gr.097857.109 · Cited by 2,353
“ural selection, such as transcription-coupled repair (Green et al. 2003), biased gene conversion (Marais 2003; Dreszer et al.”
BackgroundGenetic drift, selection and the evolution of the mutation rate
Lynch, M., Ackerman, M. S., Gout, J.-F., Long, H., Sung, W., Thomas, W. K., & Foster, P. L. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.104 · Cited by 911
R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters
Ginno, P. A., Lott, P. C., Christensen, H. C., Korf, I. F., & Chedin, F. L. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.01.017 · Cited by 930
“Likewise, global R loop formation is consistent with prior suggestions that the compositional asymmetries observed at human promoters are due to transcription-coupled mutational processes (Green et al., 2003; Polak and Arndt, 2008).”
Hearing silence: non-neutral evolution at synonymous sites in mammals
Chamary, J., Parmley, J. L., & Hurst, L. D. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1770 · Cited by 827
“First, only transcribed genes will experience biases that are associated with transcriptionally coupled mutation and repai”
BackgroundGenome instability: a mechanistic view of its causes and consequences
Aguilera, A., & Gómez‐González, B. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2268 · Cited by 830
“5-Mb fragment of a human chromosome containing seven genes, with orthologous regions in eight other mammalian species, revealed a mutational strand asymmetry that is consistent with an evolutionary shaping of each genome by transcription that has produced an excess of G and T over A and C on the coding strands in most…”
Background
Metadata
- Authors
- Program, N. C. S., Green, P., Ewing, B., Miller, W., Thomas, P. J., & Green, E. D.
- Affiliations
- Howard Hughes Medical Institute (US)
- Pennsylvania State University (US)
- National Institutes of Health (US)
- Corresponding author
- Green, Phil
- ORCID
- Green, Eric D.
- Venue
- Nature Genetics
- Published
- 2003-03-03
- Volume
- 33
- Issue
- 4
- Pages
- 514-517
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2087627409
- Cited by
- 285
- References
- 29
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 5 · 2023: 5 · 2022: 4 · 2021: 12 · 2020: 9 · 2019: 6 · 2018: 5 · 2017: 10 · 2016: 16 · 2015: 15 · 2014: 13 · 2013: 18 · 2012: 18
- FWCI
- 5.89
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health
- National Human Genome Research Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- strand asymmetry, cytosine deamination, transcription-coupled repair, germ cells, compositional asymmetry, GC content, DNA replication, mammalian evolution, nucleotide substitution rates
- MeSH terms
- Animals, Chromosomes, Human, Pair 22, DNA Mutational Analysis, Biological Evolution, Humans, Models, Genetic, Papio, RNA, Messenger, Transcription, Genetic, Sequence Analysis, DNA, CpG Islands, Cell Lineage, Databases as Topic
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