No abstract

SUMMARY Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning.

In our study, we surveyed the methylomes of 86 gene-silencing mutants by whole-genome bisulfite sequencing (BS-seq) and revealed interactions between DNA methylation pathways as well as new regulators of DNA methylation. One of the observations that we made was that mutation in histone deacetylase 6 (HDA6) resulted in loss of methylation at a small subset of sites in the genome. It has recently come to our attention that our hda6 mutant line was contaminated and thus our hda6 mutant data set did not represent data for a null mutation of HDA6. We therefore repeated the BS-seq experiments using two different hda6 mutant alleles, hda6-6 and hda6-7 (seeds generously provided by Craig Pikaard), as well as an additional wild-type control. In contrast to the limited subset of sequences that we had initially reported to be affected, we found global reduction of methylation primarily at cytosines in CHG and CHH (H = A, T, or C) sequence contexts across the genome. We would therefore now conclude, as reflected in a corrected panel of the original Figure 4A below, that HDA6 plays a stronger role in regulating methylation than what we had reported and appears to be an important factor shaping the Arabidopsis methylome, consistent with a recent study (Blevins et al., 2014). We have deposited the new sequencing data to GEO (GEO: GSE39901) and have updated our genome browser (http:// genomes.mcdb.ucla.edu/AthBSseq/). We regret this error and apologize for any inconvenience this may have caused.