RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena

Abstract

Methylated H3K27 is an important mark for Polycomb group (PcG) protein-mediated transcriptional gene silencing (TGS) in multicellular eukaryotes. Here a Drosophila E(z) homolog, EZL1, is characterized in the ciliated protozoan Tetrahymena thermophila and is shown to be responsible for H3K27 methylation associated with developmentally regulated heterochromatin formation and DNA elimination. Importantly, Ezl1p-catalyzed H3K27 methylation occurs in an RNA interference (RNAi)-dependent manner. H3K27 methylation also regulates H3K9 methylation in these processes. Furthermore, an "effector" of programmed DNA elimination, the chromodomain protein Pdd1p, is shown to bind both K27-and K9-methylated H3. These studies provide a framework for an RNAi-dependent, Polycomb group protein-mediated heterochromatin formation pathway in Tetrahymena and underscore the connection between the two highly conserved machineries in eukaryotes.[Keywords: RNA interference; H3K27 methylation; Polycomb group proteins; heterochromatin; DNA elimination] Supplemental material is available at http://www.genesdev.org.

Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway

“…However, these studies could not address identification of specific repressive histone marks as the reagents for the study were not available. It has been reported in other biological systems that enrichment of methylated H3K27 associates with gene repression (14,43). Using newly generated reagents, we have identified that E. histolytica also contains this repressive epigenetic mark, which deposits at RNAi-silenced loci.…”

“…However, conserved lysine residues, which are targets for post-translational modifications, are maintained in the E. histolytica histone H3 tail. In higher eukaryotes, enrichment of methylated H3K27 is associated with gene repression (13,14,43,44). Hence, we asked whether coupling of H3K27 methylation and transcriptional gene silencing is conserved in E. histolytica.…”

“…Dimethylation of Lysine 27 of Histone H3 Is a Repressive Epigenetic Mark in E. histolytica-Cross-talk between RNAi and H3K27 methylation leads to gene repression through heterochromatin condensation in multiple systems (14,43). To determine whether H3K27Me2 associates with the condensed chromatin in E. histolytica, we performed immunofluorescence analysis.…”

Dicer independent small RNAs associate with telomeric heterochromatin

“…Direct roles of small RNAs in the propagation of heterochromatin have been established in several eukaryotic systems, including Tetrahymena, fission yeast, and Drosophila (Moazed et al 2006;Zofall and Grewal 2006;Liu et al 2007). However, the case remains unresolved in mammalian cells, in large part due to the difficulty of detecting small RNAs homologous to heterochromatin regions, especially in somatic cells.…”

RNA regulation of epigenetic processes

“…Similar processes are involved in heterochromatin formation and programmed DNA elimination in ciliates, (35,36) as well as heterochromatin formation and nucleolar organization in Drosophila. (18,37) The nuclear organization of chromatin insulators and chromatin domains is also affected by the RNAi machinery (38) and recent deep sequencing studies have…”