Perinuclear Anchoring of H3K9-Methylated Chromatin Stabilizes Induced Cell Fate in C. elegans Embryos

Abstract

Interphase chromatin is organized in distinct nuclear sub-compartments, reflecting its degree of compaction and transcriptional status. In Caenorhabditis elegans embryos, H3K9 methylation is necessary to silence and to anchor repeat-rich heterochromatin at the nuclear periphery. In a screen for perinuclear anchors of heterochromatin, we identified a previously uncharacterized C. elegans chromodomain protein, CEC-4. CEC-4 binds preferentially mono-, di-, or tri-methylated H3K9 and localizes at the nuclear envelope independently of H3K9 methylation and nuclear lamin. CEC-4 is necessary for endogenous heterochromatin anchoring, but not for transcriptional repression, in contrast to other known H3K9 methyl-binders in worms, which mediate gene repression but not perinuclear anchoring. When we ectopically induce a muscle differentiation program in embryos, cec-4 mutants fail to commit fully to muscle cell fate. This suggests that perinuclear sequestration of chromatin during development helps restrict cell differentiation programs by stabilizing commitment to a specific cell fate. PAPERCLIP.

Cell Biology of the Caenorhabditis elegans Nucleus

“…In the set-25; met-2 and cec-4 mutants described above, detachment from the nuclear periphery did generally not result in activation of repressed genes (Towbin et al 2012;Gonzalez-Sandoval et al 2015). In contrast, inactivation of LMN-1, which also results in detachment of chromatin from the nuclear periphery, does lead to gene derepression, at least when it comes to a promoter present on a gene array (Mattout et al 2011).…”

“…Using an RNAi screen against proteins that contain a motif that recognizes methylated histones, Gonzalez-Sandoval et al (2015) searched for a protein that, when inactivated, leads to mislocalization of peripheral chromatin in embryos. This led to the identification of a chromodomain protein, CEC-4, that fits the bill (Figure 14): CEC-4 localizes to the NE, binds specifically methylated H3K9 through its chromodomain, and in its absence a marked heterochromatic domain fails to maintain its peripheral localization (Gonzalez-Sandoval et al 2015).…”

“…Using an RNAi screen against proteins that contain a motif that recognizes methylated histones, Gonzalez-Sandoval et al (2015) searched for a protein that, when inactivated, leads to mislocalization of peripheral chromatin in embryos. This led to the identification of a chromodomain protein, CEC-4, that fits the bill (Figure 14): CEC-4 localizes to the NE, binds specifically methylated H3K9 through its chromodomain, and in its absence a marked heterochromatic domain fails to maintain its peripheral localization (Gonzalez-Sandoval et al 2015). However, unlike the inactivation of both MET-2 and SET-25, which results in both derepression and detachment of chromatin from the nuclear periphery (Towbin et al 2012), the absence of CEC-4 resulted in detachment of heterochromatin from the nuclear periphery without activation of transcription.…”

“…Thus, gene expression and localization can be decoupled. Finally, while CEC-4 is needed for peripheral chromatin localization in the embryo, its function is either redundant with a yet-unknown protein(s) or not needed in later developmental stages (Gonzalez-Sandoval et al 2015) as mutants lacking CEC-4 develop normally, despite changes to chromatin organization in the embryo. However, cec-4 null mutants did show developmental defects in a system where muscle tissue was ectopically induced (see below).…”

“…The challenge of addressing this question is that inactivating factors required for this localization, such as lamins or histone modifying genes, will likely have pleiotropic effects. However, a unique opportunity came about with the discovery of CEC-4, which seems to be specific for interactions of H3K9me3 with the periphery and yet has no effect on gene expression (Gonzalez-Sandoval et al 2015). To address whether nuclear positioning may have an effect on differentiation, Gonzalez-Sandoval et al induced a pulse of HLH-1, a master regulator of muscle differentiation, throughout the entire embryo in either wild-type or cec-4 null-mutant embryos.…”