cross-linked Chromatin was sonicated with a Bioruptor targeted ShapeMap on nascent RNA: IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). Precipitated RNA was treated with 1M7 or DMS. RNA was purified by Trizol extraction. Prufied RNA was random primed and cDNA was PCR enriched for the 3' region of RD hisone transcripts and the 5' region of 18S rRNA. PCR fragments were converted to sequencing libraries using ChIP-seq library construction protocol. ChIP-seq: 1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.