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Related Concept Videos

Epigenetic Regulation01:37

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
Epigenetic Regulation01:46

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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Mutations01:39

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Updated: Jun 3, 2026

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
09:42

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Published on: September 7, 2017

Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.

Sheel Chandra1, Ziyue Gao2

  • 1Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

Plos Genetics
|June 1, 2026
PubMed
Summary

CpG mutation rates vary based on DNA sequence context and cytosine methylation. Upstream adenine significantly increases CpG mutation rates, with conserved effects across species, while methylation-specific changes suggest recent evolutionary adaptations.

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Area of Science:

  • Genetics
  • Genomics
  • Evolutionary Biology

Background:

  • Mutation rate variation is influenced by sequence context, notably at CpG sites due to cytosine methylation.
  • While methylation is a known factor, flanking sequences also affect CpG mutation rates, with incomplete correlation to methylation levels.

Purpose of the Study:

  • To precisely quantify CpG mutation rates and the mutagenic impact of methylation across diverse sequence contexts.
  • To investigate how sequence context, methylation, and their interactions shape mutation patterns in the human genome.

Main Methods:

  • Utilized a regression framework accounting for recurrent mutations to analyze human polymorphism data from the gnomAD dataset.
  • Estimated mutation rates for both unmethylated and methylated CpGs within specific 4-mer and 6-mer sequence contexts.

Main Results:

  • CpG mutation rate variation is determined by methylation status, flanking nucleotides, and their interactions, indicating distinct patterns for methylated and unmethylated CpGs.
  • Upstream sequences, particularly adenine, substantially elevate CpG mutation rates irrespective of methylation or downstream sequences.
  • Sequence context effects on CpG mutability show conservation across human, chimpanzee, and rhesus macaque, but species-specific differences, especially in methylation effects on the chimpanzee lineage, suggest recent evolutionary changes.

Conclusions:

  • Sequence context and methylation are key drivers of CpG mutation rate variation, with upstream sequences playing a significant role.
  • Conserved sequence features influence CpG mutability, while inter-species variations highlight recent evolutionary adaptations in DNA repair and demethylation pathways.