ArticlePLoS genetics2012
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 87 citations in OpenAlex.
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- SVFX: a machine learning framework to quantify the pathogenicity of structural variants.Genome biology · 2020Article
- Association of CNVs with methylation variation.NPJ genomic medicine · 2020Article
- Genome-wide DNA methylation profiling of human diabetic peripheral neuropathy in subjects with type 2 diabetes mellitus.Epigenetics · 2019Article
- 5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder.Human molecular genetics · 2018Article
- Patterns and mechanisms of structural variations in human cancer.Experimental & molecular medicine · 2018Review
- Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.Genome research · 2018Article
- A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features.BMC genomics · 2018Article
- CNVs are associated with genomic architecture in a songbird.BMC genomics · 2018Article
- Low salinity affects cellularity, DNA methylation, and mRNA expression of igf1 in the liver of half smooth tongue sole (Cynoglossus semilaevis).Fish physiology and biochemistry · 2017Article
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- Tissue-specific methylation profile in obese patients with type 2 diabetes before and after Roux-en-Y gastric bypass.Diabetology & metabolic syndrome · 2017Review
- Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.Cell reports · 2016Article
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- Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment: A Scientific Statement From the American Heart Association.Circulation. Cardiovascular genetics · 2016Review
- Preservation of methylated CpG dinucleotides in human CpG islands.Biology direct · 2016Article
- Principles Governing DNA Methylation during Neuronal Lineage and Subtype Specification.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2016Article
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Authors and funding
15 authors at 3 institutions in 2 countries.
Funding
Abstract
The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ~1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH) chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR-mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease.
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