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

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.

SUBMITTER: Sahlen P

PROVIDER: S-EPMC4557751 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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

Sahlén Pelin P Abdullayev Ilgar I Ramsköld Daniel D Matskova Liudmila L Rilakovic Nemanja N Lötstedt Britta B Albert Thomas J TJ Lundeberg Joakim J Sandberg Rickard R

Genome biology 20150803

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 ...[more]

PMID: 26313521

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