CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

We performed Chromatin Interaction Analysis by Paired-End-Tag sequencing to elucidate CTCF-mediated long range interactions. 1,480 cis and 336 trans interacting loci were identified with high reproducibility. Associating these chromatin interaction loci with histone marks, RNA Pol II, p300 and Lamin B genome wide profiles, we uncover five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and may influence proper gene expression through extensive crosstalk between promoters and regulatory elements. Chromatin interaction analysis coupled with Pair End Tags of CTCF: ChIP using anti CTCF antibody, followed by close proximity ligations. ChIP-Seq was used map RNA Pol II, p300, Lamin B genome wide profiles