Changes in DNA methylation can produce meiotically stable epialleles that affect transcription
and morphology, but the rates of spontaneous gain or loss of DNA methylation are unknown. We
examined spontaneously occurring variation in DNA methylation in Arabidopsis thaliana plants
propagated by single-seed descent for 30 generations. 114,287 CG single methylation polymorphisms
(SMPs) and 2,485 CG differentially methylated regions (DMRs) were identified, both of which show
patterns of divergence compared to the ancestral state. Many identified epialleles require MET1 or
ROS1/DEMETER-LIKE1/2 to maintain their methylation status, indicating that these epialleles may arise
through incomplete reprogramming during postfertilization. Thus, transgenerational epigenetic variation
in DNA methylation may generate new allelic states that alter transcription providing a mechanism for
phenotypic diversity in the absence of genetic mutation.
Robert J. Schmitz1,2, Matthew D. Schultz1,2,3, Mathew G. Lewsey1,2, Ronan C. O’Malley2, Mark A.
Urich1,2, Ondrej Libiger4, Nicholas J. Schork4 and Joseph R. Ecker1,2,5*
1Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
2Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
3Bioinformatics Program, University of California at San Diego, La Jolla, CA, 92093, USA.
4The Scripps Translational Science Institute and the Department of Molecular and Experimental
Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
5Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines
Road, La Jolla, California 92037, USA
Copyright. All Rights Reserved.