Chromatin-seq and RNA-seq of dREAM subunit deficient Drosophila S2R+ cells

dREAM is a multi-functional complex which activates and represses genes involved in the G2/M transition and is involved in maintaining chromatin boundaries through interactions with CTCF and BEAF-32, however the mechanisms by which it carries out gene and chromatin regulation is yet to be uncovered. Applying a novel Mnase-seq technique, RNAi and RNA-seq we report links between transcriptional changes in S2R+ cells deficient for dREAM subunits and changes in chromatin structure. The most distinct chromatin phenotype of these cells are at CTCF binding sites, several of which are located between divergent gene pairs which show impaired regulation in cells deficient for a dREAM component. S2R+ cells treated with dsRNA against GFP (control), mip40, E2F2, mip120 or mip130 where harvested for chromatin digestion by Micrococcal nuclease, or for total RNA purification. Purified DNA or RNA was then sequenced using an Illumina HiSeq 2000 machine. All samples were carried out in duplicate except E2F2, of which there is a single sample.