Genome-wide maps of histone PTMs and co-factors in pluripotent mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs)

We report here the genome wide mapping of histone PTMs and chromatin bound factors in pluripotent control and H3K27R base edited mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs) using ChIP-Seq technology. We have deposited results from chromatin immunoprecipitations done using antibodies against Rpb1 (Pol-II), Med1,H3.3, H3K27me1, H3K27me2, H3K27me3 and H3K27ac (rabbit and mouse monoclonal antibodies). We show the loss of all H3K27 from H3.1/2/3 results in loss of associated K27 methylation and acetylation as expected. In such cells, there are only modest changes to MED1 or RNA Pol-II binding or activity that correlate with transcriptional status, suggesting that H3K27ac is not required to initiate or maintain transcription of genes, while loss of H3K27me3 associates with derepression of Polycomb target genes. Overall design: 100 ug, 200 ug and 1 mg were input chromatin amounts used for histone PTM, Rpb1 (Pol-II) and Med1 ChIPs. 5% Drosophila chromatin was spiked in during immunoprecipitations for IP normalization in addition to standard FPKM normalization. Comparisons were performed between control mESCs (ABE) and two independent clones that were either mutant for only canonical H3K27 (cK27R) or all H3K27 (pK27R). In addition, we sequenced one input sample from control mESCs and EpiLCs to represent the different input chromatin amounts during immunoprecipitation. ChIP signal intensities quantified across enhancers and non-redundant genes are deposited. The non-redundant UCSC genes regionset is used from Sankar et al., Nature Cell Biology 2020 (PMID: 32231309). The enhancers defined in mouse ESCs from Whyte et al., Cell 2013 (PMID: 23582322) and in EpiLCs (H3K27ac+, H3K4me1+ and p300+ peaks) from Buecker et al., Cell Stem Cell 2014 (PMID: 24905168) were lifted over to corresponding mm10 genomic co-ordinates prior to downstream global analysis.