ArticleGenome research2008
Transcription induces strand-specific mutations at the 5' end of human genes.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed.
- Transcription start sites experience a high influx of heritable variants fueled by early development.Nature communications · 2025Article
- Article
- Mechanisms underlying low mutation rates in mammalian oocytes and preimplantation embryos.Nucleic acids research · 2025Review
- Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models.Research square · 2025Article
- Selective Effect of DNA N6-Methyladenosine Modification on Transcriptional Genetic Variations in East Asian Samples.International journal of molecular sciences · 2024Article
- The GC-content at the 5' ends of human protein-coding genes is undergoing mutational decay.Genome biology · 2024Article
- Analysis of Nucleotide Variations in Human G-Quadruplex Forming Regions Associated with Disease States.Genes · 2023Article
- The RNA m5C modification in R-loops as an off switch of Alt-NHEJ.Nature communications · 2023Article
- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
- Surveying mutation density patterns around specific genomic features.Genome research · 2022Article
- How Can We Resolve Lewontin's Paradox?Genome biology and evolution · 2022Article
- Article
- Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups.Journal of molecular evolution · 2022Article
- Non-Darwinian Molecular Biology.Frontiers in genetics · 2022Review
- Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1.Oncotarget · 2022Article
- The origin of human mutation in light of genomic data.Nature reviews. Genetics · 2021Review
- Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods.Journal of visualized experiments : JoVE · 2021Article
- Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.Nucleic acids research · 2021Article
- Evolutionary advantage of anti-parallel strand orientation of duplex DNA.Scientific reports · 2020Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A regional analysis of nucleotide substitution rates along human genes and their flanking regions allows us to quantify the effect of mutational mechanisms associated with transcription in germ line cells. Our analysis reveals three distinct patterns of substitution rates. First, a sharp decline in the deamination rate of methylated CpG dinucleotides, which is observed in the vicinity of the 5' end of genes. Second, a strand asymmetry in complementary substitution rates, which extends from the 5' end to 1 kbp downstream from the 3' end, associated with transcription-coupled repair. Finally, a localized strand asymmetry, an excess of C-->T over G-->A substitution in the nontemplate strand confined to the first 1-2 kbp downstream of the 5' end of genes. We hypothesize that higher exposure of the nontemplate strand near the 5' end of genes leads to a higher cytosine deamination rate. Up to now, only the somatic hypermutation (SHM) pathway has been known to mediate localized and strand-specific mutagenic processes associated with transcription in mammalia. The mutational patterns in SHM are induced by cytosine deaminase, which just targets single-stranded DNA. This DNA conformation is induced by R-loops, which preferentially occur at the 5' ends of genes. We predict that R-loops are extensively formed in the beginning of transcribed regions in germ line cells.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.