Skip to main content
construction release_alert
Scholars@Duke will be undergoing maintenance April 11-15. Some features may be unavailable during this time.
cancel

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.

Publication ,  Journal Article
Gertz, J; Varley, KE; Reddy, TE; Bowling, KM; Pauli, F; Parker, SL; Kucera, KS; Willard, HF; Myers, RM
Published in: PLoS Genet
August 2011

The methylation of cytosines in CpG dinucleotides is essential for cellular differentiation and the progression of many cancers, and it plays an important role in gametic imprinting. To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family. We observed that 8.1% of heterozygous SNPs are associated with differential methylation in cis, which provides a robust signature for Mendelian transmission and relatedness. The vast majority of differential methylation between homologous chromosomes (>92%) occurs on a particular haplotype as opposed to being associated with the gender of the parent of origin, indicating that genotype affects DNA methylation of far more loci than does gametic imprinting. We found that 75% of genotype-dependent differential methylation events in the family are also seen in unrelated individuals and that overall genotype can explain 80% of the variation in DNA methylation. These events are under-represented in CpG islands, enriched in intergenic regions, and located in regions of low evolutionary conservation. Even though they are generally not in functionally constrained regions, 22% (twice as many as expected by chance) of genes harboring genotype-dependent DNA methylation exhibited allele-specific gene expression as measured by RNA-seq of a lymphoblastoid cell line, indicating that some of these events are associated with gene expression differences. Overall, our results demonstrate that the influence of genotype on patterns of DNA methylation is widespread in the genome and greatly exceeds the influence of imprinting on genome-wide methylation patterns.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

August 2011

Volume

7

Issue

8

Start / End Page

e1002228

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Polymorphism, Single Nucleotide
  • Pedigree
  • Molecular Sequence Data
  • Male
  • Humans
  • Heredity
  • Gene Silencing
  • Gene Expression
  • Female
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Gertz, J., Varley, K. E., Reddy, T. E., Bowling, K. M., Pauli, F., Parker, S. L., … Myers, R. M. (2011). Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet, 7(8), e1002228. https://doi.org/10.1371/journal.pgen.1002228
Gertz, Jason, Katherine E. Varley, Timothy E. Reddy, Kevin M. Bowling, Florencia Pauli, Stephanie L. Parker, Katerina S. Kucera, Huntington F. Willard, and Richard M. Myers. “Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.PLoS Genet 7, no. 8 (August 2011): e1002228. https://doi.org/10.1371/journal.pgen.1002228.
Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 2011 Aug;7(8):e1002228.
Gertz, Jason, et al. “Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.PLoS Genet, vol. 7, no. 8, Aug. 2011, p. e1002228. Pubmed, doi:10.1371/journal.pgen.1002228.
Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 2011 Aug;7(8):e1002228.

Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

August 2011

Volume

7

Issue

8

Start / End Page

e1002228

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Polymorphism, Single Nucleotide
  • Pedigree
  • Molecular Sequence Data
  • Male
  • Humans
  • Heredity
  • Gene Silencing
  • Gene Expression
  • Female