SUVH2 and SUVH9 Couple Two Essential Steps for Transcriptional Gene Silencing in Arabidopsis

Abstract

In Arabidopsis, an RNA-directed DNA methylation pathway (RdDM) is responsible for de novo establishment of DNA methylation and contributes to transcriptional gene silencing. Recently, the microrchidia (MORC)-type ATPases were shown to play essential roles in enforcing transcriptional gene silencing of a subset of genes and transposons by regulating the formation of higher-order chromatin architecture. However, how MORC proteins cooperate with the RdDM pathway components to regulate gene expression remains largely unclear. In this study, SUVH9 and MORC6 were identified from a screening of suppressors of idm1, which is a mutant defective in active DNA demethylation. SUVH9 and MORC6 are required for silencing of two reporter genes and some endogenous genes without enhancing DNA methylation levels. SUVH9, one of SU(VAR)3-9 homologs involved in RdDM, directly interacts with MORC6 and its two close homologs, MORC1 and MORC2. Similar to MORC6, SUVH9 and its homolog SUVH2 are required for heterochromatin condensation and formation of 3D chromatin architecture at SDC and Solo-LTR loci. We propose that SUVH2 and SUVH9 bind to the methylated DNA and facilitate the recruitment of a chromatin-remodeling complex to the target loci in association with MORC proteins.

Functional Dissection of the Pol V Largest Subunit CTD in RNA-Directed DNA Methylation

“…Mutants with severe methylation defects, clustering with nrpe1-11 , include NRPE1 with the full CTD deleted (Δ1251–1976), NRPE1 missing the DeCL and QS subdomains (Δ1736–1976) and several mutants defective for proteins implicated in Pol V recruitment to target sites, including drd1 , dms3 , and suvh2 suvh9 (Jing et al, 2016; Johnson et al, 2014; Liu et al, 2014; Wierzbicki et al, 2008; Wierzbicki et al, 2009; Zhong et al, 2012) (Figure 4A, Table S2). Mutants with less severe effects on methylation, resembling CTD deletion mutants lacking the linker, 17 aa repeat, or QS subdomains, include mutants defective for proteins that interact with Pol V transcripts and/or Pol V transcription elongation complexes, including the IDN2-IDP complex ( idn2 idnl1 idnl2 ) , spt5L ( also known as ktf1) , and rrp6L1 , (Ausin et al, 2009; Bies-Etheve et al, 2009; He et al, 2009; Kollen et al, 2015; Rowley et al, 2011; Zhang et al, 2012) (Figure 4A, Table S2).…”

The RNAs of RNA-directed DNA methylation

“…However, in this case, the methylated DNA is recognized directly by the methylcytosine binding proteins, SUVH2 and SUVH9 (Johnson et al 2008; Johnson et al 2014; Liu et al 2014; Jing et al 2016; Liu et al 2016). These proteins are members of the histone methyltransferase family that have SRA domains for binding methylated DNA as well as domains for methylating histone H3 within associated nucleosomes.…”

A group of SUVH methyl‐DNA binding proteins regulate expression of the DNA demethylase ROS1 in Arabidopsis

“…In contrast, pre‐SET/SET/post‐SET domains in SUVH2 and SUVH9 have no methyltransferase activity, but interact with the DDR complex and mediate Pol V recruitment in the RdDM pathway (Johnson et al ; Liu et al ). They also interact with MORC proteins to recruit a chromatin‐remodeling complex to condense chromatin (Jing et al ). Our work here showed that SUVH1, SUVH3, SUVH7 and SUVH8 have critical roles in anti‐silencing.…”