Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription

Abstract

Heterochromatic DNA domains play important roles in regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway1–9. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and tri-methylation (H3K9me2 and H3K9me3, respectively) and heterochromatin formation10–17. H3K9me is in turn required for recruitment of RNAi to chromatin to promote sRNA amplification11,15,18. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast S. pombe homolog of mammalian SUV39H H3K9 methyltransferases, we designed active site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing (CTGS) at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defense.

The Methyltransferase AflSet1 Is Involved in Fungal Morphogenesis, AFB1 Biosynthesis, and Virulence of Aspergillus flavus

“…Di-and tri-methylation at H3K4 are typical epigenetic signature for gene activation (Jambhekar et al, 2019). The previous study showed that the methylation of H3K9 is associated with transcriptional repressed loci, and that different from H3K9me3 which is associated with transcriptional silence, H3K9me2 is associated with transcriptional activation (Liu et al, 2015;Jih et al, 2017). H3K9me2 loci contain euchromatic transcription associated modifications, and couple transcript degradation via RNAi to the establishment of H3K9 methylation loci (Jih et al, 2017).…”

“…The previous study showed that the methylation of H3K9 is associated with transcriptional repressed loci, and that different from H3K9me3 which is associated with transcriptional silence, H3K9me2 is associated with transcriptional activation (Liu et al, 2015;Jih et al, 2017). H3K9me2 loci contain euchromatic transcription associated modifications, and couple transcript degradation via RNAi to the establishment of H3K9 methylation loci (Jih et al, 2017). The results of the study supposed that, mainly by catalyzing the di-and trimethylation of H3K4 and involving the dimethylation of H3K9, AflSet1 up-regulated fungal development, secondary metabolism, and virulence principally via positive regulation of orthodox conidiation, sclerotia formation, and aflatoxin biosynthesis pathways.…”

A heterochromatic histone methyltransferase lowers nucleosome occupancy at euchromatic promoters

“…Nucleosomes were disrupted and expression of piRNAs and transposons increased, however it was impossible to know which modification was responsible for which function. An independent study found that H3K9me2 and H3K9me3 were functionally distinct in S. pombe where H3K9me2 domains were transcriptionally active and coupled RNAimediated silencing to establish silent H3K9me3 domains (Jih et al 2017). In this study, we examine the defects associated with selective loss of H3K9me3, leaving H3K9me1 and H3K9me2 intact.…”

Cell differentiation: What have we learned in 50 years?

“…A last important holozoan gene regulatory functionality is the "silencing" of gene expression carried by the histone methylating enzymes SUV39H and the Polycomb Group II proteins (Jih et al, 2017). Though acting on the write-read-rewrite mechanism common to all eukaryotes, silencing by methylation is a synapomorphy of Opisthokonta, having arisen in a common ancestor of holozoans and fungi (Kingston and Tamkun, 2014;Steffen and Ringrose, 2014).…”