The control of gene expression and cell identity by H3K9 trimethylation

Abstract

Histone 3 lysine 9 trimethylation (H3K9me3) is a conserved histone modification that is best known for its role in constitutive heterochromatin formation and the repression of repetitive DNA elements. More recently, it has become evident that H3K9me3 is also deposited at certain loci in a tissue-specific manner and plays important roles in regulating cell identity. Notably, H3K9me3 can repress genes encoding silencing factors, pointing to a fundamental principle of repressive chromatin auto-regulation. Interestingly, recent studies have shown that H3K9me3 deposition requires protein SUMOylation in different contexts, suggesting that the SUMO pathway functions as an important module in gene silencing and heterochromatin formation. In this Review, we discuss the role of H3K9me3 in gene regulation in various systems and the molecular mechanisms that guide the silencing machinery to target loci.

Keywords: Cell fate maintenance; Chromatin; Epigenetics; Gene regulation; Germline; Heterochromatin; Transcriptional repression; Transposons.

Fig. 1.

Schematic of enzymatic machineries involved in H3K9me3 regulation. H3K9me3 (yellow star) is deposited by ‘writers’ and is recognized by the chromodomain present in numerous ‘reader’ proteins, which include the HP1 family of proteins. It is removed by ‘erasers’ from the JmjC-domain family of demethylases. The table depicts species-specific H3K9me3 writers. *G9a primarily acts as a H3K9 mono- and dimethylase, but can catalyze H3K9 trimethylation in vitro with slow kinetics (Collins et al., 2005).

Fig. 2.

Modes of recruiting the H3K9me3 machinery to specific genomic targets. Target specificity for recruitment of HMTs is either provided by: (A) DNA-binding proteins with sequence-specific DNA binding motifs; or (B) by small non-coding RNAs associated with Argonaute proteins.

Fig. 3.

The SUMO pathway is involved in SetDB1-dependent H3K9me3 deposition downstream of different silencing pathways. (A) Model of KRAB-ZFP/KAP1-mediated TE silencing in human cells. KRAB-ZFPs recognize specific TE sequences in DNA. The KRAB-ZFP co-repressor KAP1 is a SUMO E3 ligase that undergoes autocatalytic SUMOylation (involving the SUMO E1 and E2 ligases). It then recruits the H3K9-specific HMT SetDB1 (via the interaction between SUMO and the SUMO-interacting motif present in SetDB1), which in turn induces methylation of H3K9. Adapted from Ivanov et al. (2007). (B) Model of piRNA-mediated TE silencing in the Drosophila female germline. piRNAs guide the Piwi complex to complementary nascent TE transcripts. The Piwi complex interacts with the SUMO E3 ligase Su(var)2-10 (Sv210), which is auto-SUMOylated and may also induce the SUMOylation of additional chromatin factors. The SUMO moiety then recruits the SetDB1/Wde (MCAF1 homolog) complex, which induces methylation of H3K9. Adapted from Ninova et al. (2019a preprint).

Fig. 4.

Auto-regulation of factors involved in H3K9me3 deposition in different systems. (A) Model of KRAB-ZFP gene autoregulation in human cells. KRAB-ZFP genes themselves are marked by H3K9me3 deposited by KRAB-ZFP-mediated recruitment of the H3K9-HMT SetDB1. Adapted from O'Geen et al. (2007). (B) Model of auto-regulation of the SetDB1 co-factor Wde in Drosophila germ cells. The wde gene is repressed through H3K9me3 accumulation that is dependent on the SetDB1/Wde complex, which thereby limits its own expression. Adapted from Ninova et al. (2019b). (C) Model of the negative feedback of Clr4 regulation and heterochromatin assembly in fission yeast. Genome-wide H3K9me3 is controlled by modulating the expression of the HMT Clr4 via accumulation of the repressive H3K9me3 mark on the clr4 gene region. Adapted from Wang et al. (2015).