For ATAC-seq method, nuclei preparation and transposition and amplification of transposed fragments for library preparation was performed as described in Corces et al, 2017 with minor modifications; (i) 70,000 cells were used per experimental condition and (ii) The DNase treatment of cells in culture medium, before the transposition reaction, was skipped. For ChIP-seq, lysates were clarified from sonicated nuclei and chromatin (in the range of 150-400 bp) was isolated and precipitated with anti-RNAPII-CTD-hypo (8WG16; 05-952, lot: 2262610) from Millipore or anti-H3K27ac (ab4729, Abcam) or anti-H3K27me3 (07-449, Millipore). For ATAC-seq method, transposition and amplification of transposed fragments for library preparation was performed using Nextera DNA Library Prep Kit (Illumina, Inc) and primers as described in Corces et al., 2017. For ChIP-Seq, DNA libraries were generated by ligation adapters and amplification by LM-PCR (Truseq) or (NEBNext). Briefly, ChiPed or Input dsDNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase as described previously (Lavigne et al., 2017). The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. Alternatively, we used NEBnext and Truseq approaches to multiplex samples for sequencing different samples in a single lane of the flowcell. qPCR with Illumina primers was used to control for overamplification. The purified DNA library was size selected by AMpure beads purification as previously described and was typically in the range of 200 to 500 bp. In all cases, libraries were sequenced on Hiseq2000 or 2500 in Genecore, EMBL following manufacturer's protocols. double-stranded single-end DNA-seq was performed for ChIP-seq, Input-seq and ATAC-seq.