Cellular fractionation was used to isolate nuclei and extract chromatin as previously described (Bhatt et al., Cell 2012).  Chromatin was resuspended in TRIzol and RNA was purified using Rneasy Columns (Qiagen). ~100ng of chromatin-associated RNA was used for library construction. RNA-seq libraries were constructed using the Illumina Stranded TruSeq Kit, adapted from the manufacturer's instructions.