Ultra-deep 3D genome structure mapping with Region Capture Micro-C

In an effort to map the deeply map the structure of the genome at loci of interest, we applied Region Capture Micro-C and revealed focal patterns of contact between enhancers & promoters that we term microcompartments. We have mapped genomic structure at 0.4-1.9 Mb-sized regions at the Klf1, Ppm1g, Fbn2, Sox2, and Nanog loci across 4 conditions: wild-type and transcriptionally inhibited mouse Embryonic Stem Cells (mESCs), and cohesin-depletion & control treatments in a RAD21-AID genome-edited mESC line. Overall design: Micro-C with capture of five genomic regions in mouse embryonic stem cells, including triptolide treatment and depletion of cohesin subunit RAD21 using the AID system and IAA treatment.