p(A)+ RNA-seq with hybrid selection: We generated RNA sequencing libraries as described in Engreitz et al. Cell 2014. We performed hybrid selection after barcoding of DNA libraries on a combined pool as described in Gnirke et al. Nature Biotech 2009. ATAC-Seq: We performed ATAC-Seq as previously described (Buenrostro JD et al. Nature Methods 2013) using 50,000 mESCs. PRO-Seq: We performed PRO-Seq essentially as described in Kwak H et al. Science 2013. ChIP-Seq: We performed ChIP-Seq as described in Busby M et al. biorXiv 2016.