Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans

Abstract

The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Lys4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss vary, suggesting additional chromatin factors contribute to context dependent effects. Using a proteomics approach, we identified CFP1 associated proteins and an unexpected direct link between Caenorhabditis elegans CFP-1 and an Rpd3/Sin3 small (SIN3S) histone deacetylase complex. Supporting a functional connection, we find that mutants of COMPASS and SIN3 complex components genetically interact and have similar phenotypic defects including misregulation of common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3S HDAC complex at promoters.

Cooperation between Caenorhabditis elegans COMPASS and condensin in germline chromatin organization

“…Whether these effects reflect a direct role in transcription, or a more general role in germline chromatin organization is not known. Significantly, we previously found no correlation between COMPASS dependent H3K4me3 at promoters and transcription in C. elegans embryos, consistent with recent observations in other organisms (26)(27)(28)(29)(30). Likewise, increased genome instability in set-2 mutant germlines was not associated with defects in the induction of the DNA damage response (DDR) pathway, suggesting downstream effects in the DNA repair process (24).…”

“…If SET-2 contributes to chromatin organization in germ cells, one prediction is that its absence might impact chromosome function and result in chromosome segregation defects in meiosis, thereby generating aneuploid cells (44). We found no evidence for such defects in set-2 mutant animals (24,30,45). What we did find, however, is that endoreplicated intestinal cells of adult animals showed chromosome segregation defects very similar to those reported in condensin-II mutants (45,46).…”

“…Based on these observations, we suggest that the presence of COMPASS at transcription sites could contribute to the organization of chromatin in these clusters. This could take place through the recruitment of an H3K4me3 reader, as described for the NCAPD3 subunit of condensin-II (111), or through the recruitment of additional proteins (30). Finally, given the recent implication of the nuclear RNAi pathway and the MORC-1 gene silencing protein in germline chromatin organization (112,113), additional interactions between COMPASS and these pathways may be involved.…”

The CONDOR pipeline for simultaneous knockdown of multiple genes identifies RBBP-5 as a germ cell reprogramming barrier inC. elegans

“…Based on the robustness of CONDOR we were able to identify the Set1/MLL methyltransferase complex member RBBP-5 (Beurton et al, 2019) as a novel germ cell reprogramming barrier. The rational for using CONDOR to screen for chromatin factors that counteract germ cell reprogramming was based on our observation that overexpression of UNC-30 in animals with RNAi against the previously identified germ cell reprogramming barrier LIN-53 (Patel et al, 2012;Seelk et al, 2016;Tursun et al, 2011) yielded only a limited number of animals with GABAergic motor neuron fate in germ cells.…”

“…Depletion of LIN-53 or PRC2 subunits resulted in a global loss of chromatin silencing in the germline as revealed by abolished H3K27 methylation (Patel et al, 2012). In contrast, it was demonstrated that RNAi against rbbp-5, which is part of the chromatin-regulating complex SET1/MLL/COMPASS (Beurton et al, 2019; Li and Kelly, 2011), reduces H3K4 methylation in the germline. Thus, the enhancement observed upon simultaneous RNAi knockdown of lin-53 together with rbbp-5 is likely due to distinct effects on germline chromatin.…”