Capture of Associated Targets on Chromatin (CATCH) Links Long-Distance Chromatin Looping to Transcriptional Coordination

We describe here a sensitive and novel method of identifying endogenous DNA-DNA interactions. Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide. The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high quality data, has excellent reproducibility and is completed in less than 24 hours. Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and estrogen receptor binding sites. In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centered near the TSS of genes, and critically, the genes identified as physically interacting are shown to be transcriptionally co-expressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programs. There are 7 bedgraph files; two are “control” samples; sets of samples were pulled from the same chromosome.