Genome-wide Promoter Capture Hi-C data reiterate previously known promoter-distal element interactions. (A) Brief schematic of CHi-C experimental pipeline. (B) Contact map generated in Seqmonk using the 2 biological replicates of Hi-C data. (C) Schematic of the CHi-C processing pipeline. Significant interactions as identified by the CHiCAGO pipeline²⁴  were loaded into the WashU browser as a custom track (interactions) along with the bigwig tracks of the previously published HPC-7 ChIP-Seq data.^17,18  Only interactions where both interacting fragments are within the genomic window are shown. For visualization purposes, the promoters used as “bait” in the CHi-C protocol are also shown (promoter fragments), the individual restriction enzyme fragments (HindIII restriction fragments) and a track showing RefSeq genes. All tracks shown are in mouse genome build mm9. (D) Scl locus; shown for verification are the previously identified regulatory elements of the Scl locus. (E) Lmo2 locus; shown for verification are the previously identified regulatory elements of the Lmo2 locus. PE, paired end.