SCIENCE@home

Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana

Dazhe Meng,M. Dubin,Pei-yue Zhang,E. Osborne,O. Stegle,Richard M. Clark,M. Nordborg

Published 2016 in PLoS Genetics

ABSTRACT

The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis-methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs.

PUBLICATION RECORD

CITATION MAP

EXTRACTION MAP

CLAIMS

  • No claims are published for this paper.

CONCEPTS

  • No concepts are published for this paper.

REFERENCES

Showing 1-54 of 54 references · Page 1 of 1

CITED BY

Showing 1-100 of 112 citing papers · Page 1 of 2

12
Next