Total RNA-Seq on control, Polycomb null and H3K27R mutant mESCs and EpiLCs

Here we report the results of total RNASeq derived transcriptomes from naïve pluripotent mouse embryonic stem cells (mESCs) and pre-gastrulation epilblast like cells (EpiLCs) derived from mESCs following a 48 hour treatment with activin, FGF and knockout serum replacement as described in Hayashi et al., Cell 2011 (PMID: 21820164). We observe a strong concordance between histone mutant (H3K27R) cell lines and Polycomb null (SUZ12 knockout) steady state mESCs, with the primary effect of mutation resulting in gene de-repression. H3K27me3 is found strongly correlated with gene repression while H3K27ac is found strongly correlative with gene expression. We also show the lack of requirement for H3K27ac for gene activation upon differentiation of promoter or enhancer mediated EpiLC gene markers, leading us to conclude that transcription occurs independently of the requirement of H3K27ac. Overall design: Transcriptomes of mESCs and EpiLCs in biological triplicates were assayed from total RNA isolated in control (ABE), SUZ12 knockout or different H3K27R mutant cell lines Processed data are in Microsoft Excel worksheets with DeSeq2 comparisons between mutant and control mESC transcriptomes, mutant EpiLCs vs respective mESC transcriptomes and quantification of relevant ChIP signals of unchanged, down or upregulated genes at the transcriptomic levels.