Cell Reports
Volume 17, Issue 8, 15 November 2016, Pages 2042-2059
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A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

https://doi.org/10.1016/j.celrep.2016.10.061Get rights and content
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Highlights

  • Integrative analysis of chromatin architecture in a broad set of human tissues

  • FIREs are an architectural feature of chromatin organization

  • FIREs are enriched for super-enhancers and show tissue-specific chromatin interactions

  • FIRE formation is partially dependent on CTCF and the Cohesin complex

Summary

The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we find topologically associating domains highly conserved in different tissues. We also discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for super-enhancers and are near tissue-specifically expressed genes. They display strong tissue-specificity in local chromatin interactions. Additionally, FIRE formation is partially dependent on CTCF and the Cohesin complex. We further show that FIREs can help annotate the function of non-coding sequence variants.

Cited by (0)

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Co-first author

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Present address: Arima Genomics Inc., 6404 Nancy Ridge Dr., San Diego, CA, 92121, USA

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Present address: Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA

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Present address: Department of Biological Sciences, KAIST, Daejeon 34141, South Korea

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Lead Contact