title: 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.
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.
authors: National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.
authors: Di
authors: D
authors: Fan
authors: Yan
authors: Y
authors: Dai
authors: Xuncheng
authors: X
authors: Wang
authors: Zhenjie
authors: Z
authors: Wang
authors: Hang
authors: H
authors: He
authors: Hongchun
authors: H
authors: Yang
authors: Ying
authors: Y
authors: Cao
authors: Xing Wang
authors: XW
authors: Deng
authors: Ligeng
authors: L
authors: Ma
mesh_terms: D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D002843:Chromatin / Q000201:enzymology; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D034741:RNA, Small Interfering / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics* / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D004268:DNA-Binding Proteins; D034741:RNA, Small Interfering; C526313:IBM1 protein, Arabidopsis; D056484:Jumonji Domain-Containing Histone Demethylases; C519655:RDR2 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; C519654:DCL3 protein, Arabidopsis; D043244:Ribonuclease III