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BioMed Central, Genome Biology, 1(16), 2015

DOI: 10.1186/s13059-015-0727-9

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

Journal article published in 2015 by Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld ORCID, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas J. Albert, Joakim Lundeberg, Rickard Sandberg ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract 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.