ChICseq analysis of active and repressive histone modifications in intestinal and non-intestinal C. elegans cells [ChIC-seq]

Endomitosis is a non-canonical cell cycle in which cells undergo all four phases of a canonical cell cycle (G1, S, G2 and M), but do not initiate or complete cytokinesis during M phase. We found that cytokinesis genes, as well as many cell-cycle genes, are transcriptionally downregulated during endomitosis of the C. elegans intestine. To understand the mechanisms underlying cell-cycle gene repression, we isolated cells from L1 larvae of a strain expressing intestinal-specific mCherry (elt-2p::mCherry-PH-P2A-H2B-mCherry) grown for one hour at 20ºC. We sorted intestinal and non-intestinal cells by FACS based on the mCherry expression. We performed ChIC-seq (or CUT&RUN) to map the H3K4me3, H3K9me3, H3K27me3 and H3K36me3 histone modifications and analyze whether promoter regions of cell-cycle genes are more enriched with active or repressive marks in intestinal cells undergoing endomitosis. ChIC-seq of H3K4me3 (3 biological replicates), H3K9me3 (2 biological replicates), H3K27me3 (3 biological replicates) and H3K36me3 (3 biological replicates) in intestinal and non-intestinal cells generated from pools of 1000 cells. A negative control where no antibodies were added (NoAb control) was performed in non-intestinal cell samples (2 biological replicates).