ArticleNucleic acids research2023
Structural underpinnings of mutation rate variations in the human genome.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.PLoS genetics · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.bioRxiv : the preprint server for biology · 2026Article
- GnT Motifs Can Increase T:A→G:C Mutation Rates Over 1000-fold in Bacteria.Molecular biology and evolution · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Ensemble learning-based predictor for driver synonymous mutation with sequence representation.PLoS computational biology · 2025Article
- kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.Computational and structural biotechnology journal · 2024Article
- Towards the genomic sequence code of DNA fragility for machine learning.Nucleic acids research · 2024Article
- RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice.Briefings in bioinformatics · 2024Article
- Effects of parental age and polymer composition on short tandem repeat de novo mutation rates.Genetics · 2024Article
- C and G are frequently mutated into T and A in coding regions of human genes.Molecular genetics and genomics : MGG · 2024Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Evolution of the Mutation Spectrum Across a Mammalian Phylogeny.Molecular biology and evolution · 2023Article
- "Evolution of the mutation spectrum across a mammalian phylogeny".bioRxiv : the preprint server for biology · 2023Article
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2 authors.
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Abstract
Single nucleotide mutation rates have critical implications for human evolution and genetic diseases. Importantly, the rates vary substantially across the genome and the principles underlying such variations remain poorly understood. A recent model explained much of this variation by considering higher-order nucleotide interactions in the 7-mer sequence context around mutated nucleotides. This model's success implicates a connection between DNA shape and mutation rates. DNA shape, i.e. structural properties like helical twist and tilt, is known to capture interactions between nucleotides within a local context. Thus, we hypothesized that changes in DNA shape features at and around mutated positions can explain mutation rate variations in the human genome. Indeed, DNA shape-based models of mutation rates showed similar or improved performance over current nucleotide sequence-based models. These models accurately characterized mutation hotspots in the human genome and revealed the shape features whose interactions underlie mutation rate variations. DNA shape also impacts mutation rates within putative functional regions like transcription factor binding sites where we find a strong association between DNA shape and position-specific mutation rates. This work demonstrates the structural underpinnings of nucleotide mutations in the human genome and lays the groundwork for future models of genetic variations to incorporate DNA shape.
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