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PLoS Genet. 2014 Sep 11;10(9):e1004585. doi: 10.1371/journal.pgen.1004585. eCollection 2014 Sep.

Hydroxymethylated cytosines are associated with elevated C to G transversion rates.

Author information

1
EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia.
2
EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain.
3
Reprogramming and Chromatin Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, London, United Kingdom.
4
Molecular Systems Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, London, United Kingdom.

Abstract

It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes. The repertoire of naturally occurring cytosine modifications, however, extends beyond 5-methylcytosine to include its oxidation derivatives, notably 5-hydroxymethylcytosine. The effects of these modifications on sequence evolution are unknown. Here, we combine base-resolution maps of methyl- and hydroxymethylcytosine in human and mouse with population genomic, divergence and somatic mutation data to show that hydroxymethylated and methylated cytosines show distinct patterns of variation and evolution. Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors. Controlling for multiple potential confounders, we find derived C to G SNPs to be 1.43-fold (1.22-fold) more common at hydroxymethylated sites compared to methylated sites in human (mouse). Increased C to G rates are evident across diverse functional and sequence contexts and, in cancer genomes, correlate with the expression of Tet enzymes and specific components of the mismatch repair pathway (MSH2, MSH6, and MBD4). Based on these and other observations we suggest that hydroxymethylation is associated with a distinct mutational burden and that the mismatch repair pathway is implicated in causing elevated transversion rates at hydroxymethylated cytosines.

PMID:
25211471
PMCID:
PMC4161303
DOI:
10.1371/journal.pgen.1004585
[Indexed for MEDLINE]
Free PMC Article
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