ChIP-seq on COMPASS-degron cells

Here, we showed that acute lost H3K4me3 induces rapid reduction in global transcription with progressively increase in magnitude over the time-course cooccurrence with lost all H3K4 methylations. To further determine the effects of COMPASS subunits degradation on H3K4 methylations occupancies genome-wide, we performed time-course spike-in chromatin immunoprecipitation and sequencing (ChIP-seq, also known as ChIP-Rx) analysis in both degron systems. Overall design: DPY30-mAID and RBBP5-FKBP degron tag into the 3' end of both alleles of endogenous Dpy30 and Rbbp5 locus of the E14 mESC cell line, respectively. The endogenous Dpy30 gene was edited to encode Auxin inducible degradation (miniAID)-BFP at the C terminus of Dpy30 in OsTir1 E14 mESCs. The endogenous Rbbp5 gene was edited to encode FKBP12 tag-Neomycin that enables targeted degradation upon dTAG-13 treatment. DPY30mAID, DPY30-mAID degron cell; DPY30mAID_Kdm5dKO, Kdm5a and Kdm5b double knock out based on DPY30-mAID degron cell; RBBP5FKBP, RBBP5-FKBP degron cell.