IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis.
Nucleic Acids Res, 2012/10;40(18):8905-16.
Fan D[1], Dai Y, Wang X, Wang Z, He H, Yang H, Cao Y, Deng XW, Ma L
Affiliations
PMID: 22772985DOI: 10.1093/nar/gks647
Impact factor: 19.16
Abstract
Small RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in Arabidopsis that controls the expression of multiple genes and several developmental processes. RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3) are necessary factors in 24-nt small interfering RNA (siRNA) biogenesis, which is part of the RdDM pathway. Here, we found that Increase in BONSAI Methylation 1 (IBM1), a conserved JmjC family histone demethylase, is directly associated with RDR2 and DCL3 chromatin. The mutation of IBM1 induced the hypermethylation of H3K9 and DNA non-CG sites within RDR2 and DCL3, which repressed their expression. A genome-wide analysis suggested that the reduction in RDR2 and DCL3 expression affected siRNA biogenesis in a locus-specific manner and disrupted RdDM-directed gene repression. Together, our results suggest that IBM1 regulates gene expression through two distinct pathways: direct association to protect genes from silencing by preventing the coupling of histone and DNA methylation, and indirect silencing of gene expression through RdDM-directed repression.
MeSH terms
Arabidopsis; Arabidopsis Proteins; Chromatin; DNA Methylation; DNA-Binding Proteins; Epigenesis, Genetic; Gene Expression Regulation, Plant; Gene Silencing; Jumonji Domain-Containing Histone Demethylases; Mutation; RNA, Small Interfering; RNA-Dependent RNA Polymerase; Ribonuclease III
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