H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity

Abstract

The developmental role of histone H3K9 methylation (H3K9me), which typifies heterochromatin, remains unclear. In Caenorhabditis elegans, loss of H3K9me leads to a highly divergent upregulation of genes with tissue and developmental-stage specificity. During development H3K9me is lost from differentiated cell type-specific genes and gained at genes expressed in earlier developmental stages or other tissues. The continuous deposition of H3K9me2 by the SETDB1 homolog MET-2 after terminal differentiation is necessary to maintain repression. In differentiated tissues, H3K9me ensures silencing by restricting the activity of a defined set of transcription factors at promoters and enhancers. Increased chromatin accessibility following the loss of H3K9me is neither sufficient nor necessary to drive transcription. Increased ATAC-seq signal and gene expression correlate at a subset of loci positioned away from the nuclear envelope, while derepressed genes at the nuclear periphery remain poorly accessible despite being transcribed. In conclusion, H3K9me deposition can confer tissue-specific gene expression and maintain the integrity of terminally differentiated muscle by restricting transcription factor activity.

SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity

“…Although several C. elegans proteins have been implicated in methylation of H3K9 (refs. 24 – 27 ), only the double deletion of genes encoding two SET domain-containing proteins, MET-2 and SET-25, eliminates all detectable H3K9me, both in embryos 6 , 7 , 28 and at later stages of somatic development 6 , 7 , 29 . The loss of H3K9me compromises the transcriptional repression of tissue-specific genes and repetitive elements 6 , 30 , although no other common histone methylation marks were altered upon met-2 and set-25 ablation 7 .…”

CUT&RUN for Chromatin Profiling in Caenorhabditis elegans

“…The CUT&RUN workflow is simple and reproducible, and has been used successfully in many model organisms (including Saccharomyces cerevisiae and Drosophila melanogaster ) as well as human cells (Skene & Henikoff, 2017; Skene, Henikoff, & Henikoff, 2018), all with well‐documented protocols available, especially for use in mammalian cells (Hainer & Fazzio, 2019; Janssens & Henikoff, 2019; Liu, 2021). The technique has only recently been utilized for the first time in Caenorhabditis elegans (Methot et al., 2021), however, and has likely not been broadly adopted in this important system because of the lack of a detailed protocol and the difficulty of dissociating worms into healthy cells. C. elegans is a widely used model organism for studying development, aging, behavior, gene regulation, chromatin biology, and more (Caldwell, Willicott, & Caldwell, 2020; Corsi, Wightman, & Chalfie, 2015; Fischer, 2010; González‐Aguilera, Palladino, & Askjaer, 2014; Kenyon, 2005; Rechavi & Lev, 2017; Sengupta & Samuel, 2009; Sulston & Horvitz, 1977; Wenzel, Palladino, & Jedrusik‐Bode, 2011), and detailed studies of chromatin biology in these contexts would be instrumental.…”

“…The CUT&RUN workflow is simple and reproducible, and has been used successfully in many model organisms (including Saccharomyces cerevisiae and Drosophila melanogaster) as well as human cells (Skene & Henikoff, 2017;Skene, Henikoff, & Henikoff, 2018), all with well-documented protocols available, especially for use in mammalian cells (Hainer & Fazzio, 2019;Janssens & Henikoff, 2019;Liu, 2021). The technique has only recently been utilized for the first time in Caenorhabditis elegans (Methot et al, 2021), however, and has likely not been broadly adopted in this important system because of the lack of a detailed protocol and the difficulty of dissociating worms 1) and dissociated into a worm chunk/cell mixture (2) using a cuticle disruption buffer and mechanical douncing in wash buffer. The worm/cell mixture is bound to concanavalin A (ConA)-coated beads (3) to facilitate the CUT&RUN protocol.…”

Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis

“…Hdac1 binds to repressive genomic regions that are facultative but not constitutive heterochromatin. Though histone modifications underlying constitutive heterochromatin have been shown to regulate developmental genes (Riddle et al, 2011; Wang et al, 2018; Methot et al, 2021), the profile of H3K27me3 is largely different (∼90% non-overlapping peaks) from profiles of H3K9me2, 3, and H4K20me3 in early Xenopus development (data not shown, partially shown in van Kruijsbergen et al, 2017). These observations suggest that Hdac1-mediated suppression is largely dictated by developmental programs.…”