CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [Hi-C]

The eleven zinc finger (ZF) protein CTCF regulates topologically associating domain (TAD) formation and transcription through selective binding to thousands of genomic sites. We replaced endogenous CTCF in mouse embryonic stem (ES) cells with GFP-tagged wildtype or mutant proteins lacking individual ZFs. We examined the various ES cell lines using next generation sequencing methods (ChIP-Seq, RNA-Seq, MedSeq, HiC) in order to identify additional determinants of CTCF positioning and function. 2) Hi-C derived from mouse ES cells expressing GFP-CTCF or a CTCF mutant protein lacking ZF8. Hi-C libraires were prepared from three biological replicates.