DNA methylation is essential for gene regulation, transposon silencing and imprinting. Although the generation of specific DNA methylation patterns is critical for these processes, how methylation is regulated at individual loci remains unclear. Here we show that a family of four putative chromatin remodeling factors, CLASSY (CLSY) 1–4, are required for both locus-specific and global regulation of DNA methylation in Arabidopsis thaliana. Mechanistically, these factors act in connection with RNA polymerase-IV (Pol-IV) to control the production of 24-nucleotide small interfering RNAs (24nt-siRNAs), which guide DNA methylation. Individually, the CLSYs regulate Pol-IV–chromatin association and 24nt-siRNA production at thousands of distinct loci, and together, they regulate essentially all 24nt-siRNAs. Depending on the CLSYs involved, this regulation relies on different repressive chromatin modifications to facilitate locus-specific control of DNA methylation. Given the conservation between methylation systems in plants and mammals, analogous pathways may operate in a broad range of organisms.
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We thank laboratory members and colleagues for comments and discussions, the Salk Institute NGS core for sequencing, the bioinformatics core for technical support, and L. and C. Greenfield for charitable contributions. This work was supported by the NIH (GM112966) and Hearst Foundation to J.L. M.Z. was funded by a Pioneer Fund Postdoctoral Award. M.Z. and A.M.S.P. were funded by postdoctoral fellowships from the Glenn Center for Aging Research at the Salk Institute. This work was also supported by the NGS Core Facility and the Integrative Genomics and Bioinformatics Core Facility at the Salk Institute with funding from NIH-NCI CCSG P30 014195, the Glenn Center for Aging Research at the Salk Institute, the Chapman Foundation and the Helmsley Charitable Trust.
The authors declare no competing interests.
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Supplementary Figures 1–9
Summary of the mRNA-seq data
Summary of the smRNA-seq data
The numbers of 21-24nt-siRNA clusters
Reduced 24nt-siRNA clusters
Down-regulated 21nt- and 22nt-siRNA clusters
Summary of the MethylC-seq data
Hypo DMRs lists
Upregulated loci in clsy and pol-iv mutants
Gene expression matrix for Fig. 4b
Summary of the ChIP-seq data
Primer oligos for qPCR in this study
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Zhou, M., Palanca, A.M.S. & Law, J.A. Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family. Nat Genet 50, 865–873 (2018). https://doi.org/10.1038/s41588-018-0115-y
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