Genome-wide histone modification and accessibility maps of mESCs, in the pluripotent state and after induced differentiation

Gene expression networks are tightly regulated by transcription factors (TF) and their targeted regulatory genomic elements (enhancers), which are known to correlate with specific histone modifications and chromatin accessibility. The identification of enhancers on a genome wide level is an important prerequisite for many functional studies, however the prediction of enhancer elements, especially with in response to changing conditions, remains challenging. Here we report the generation of a genome-wide mESC enhancer prediction map, comparing the pluripotent state and induced differentiation, by the integration of data on transcription, chromatin accessibility and multiple histone modifications. Overall design: mESCs, in the pluripotent state or after induced differentiation, were assessed for genome-wide changes in (i) gene expression by RNA-seq for poly-adenylated transcripts using biological triplicates, (ii) chromatin accessibility by ATAC-seq, and (iii) enrichment of eight specific chromatin marks by ChIP-seq.