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Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution

2015; BioMed Central; Volume: 16; Issue: 1 Linguagem: Inglês

10.1186/s13059-015-0727-9

1474-760X

Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas J. Albert, Joakim Lundeberg, Rickard Sandberg,

RNA and protein synthesis mechanisms

Although the locations of promoters and enhancers have been identified in several cell types, we still have limited information on their connectivity. We developed HiCap, which combines a 4-cutter restriction enzyme Hi-C with sequence capture of promoter regions. Applying the method to mouse embryonic stem cells, we identified promoter-anchored interactions involving 15,905 promoters and 71,984 distal regions. The distal regions were enriched for enhancer marks and transcription, and had a mean fragment size of only 699 bp — close to single-enhancer resolution. High-resolution maps of promoter-anchored interactions with HiCap will be important for detailed characterizations of chromatin interaction landscapes.