@article{6065d7ec10a742eeb07bbc2728ccee79,
title = "A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome",
abstract = "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.",
author = "Schmitt, {Anthony D.} and Ming Hu and Inkyung Jung and Zheng Xu and Yunjiang Qiu and Tan, {Catherine L.} and Yun Li and Shin Lin and Yiing Lin and Barr, {Cathy L.} and Bing Ren",
note = "Funding Information: We would like to dedicate this manuscript in loving memory of Joseph Schmitt. We would like to give special thanks to Samantha Kuan and Bin Li for operation of the sequencing instruments and data processing. We{\textquoteright}d like to acknowledge the help of Michael Yu from Trey Ideker{\textquoteright}s laboratory (UCSD), Doug Chapski from Tom Vondriska{\textquoteright}s laboratory (UCLA), and Jesse Dixon (Salk Institute) for sharing helpful files or codes to facilitate this study. We would also like to give special thanks to David Gorkin for numerous helpful discussions throughout the project, as well as the additional members of the Ren laboratory. This work is supported by the Ludwig Institute for Cancer Research and grants from NIH ( U54DK107977 to B.R. and M.H. and R01 ES024984 to B.R.). A.D.S. is supported by an NIH genetics training grant T32 GM008666 . C.L.B. is supported by funding from The Ontario Mental Health Foundation , The Krembil Foundation , and The Hospital for Sick Children Psychiatric Endowment Fund . Y. Li and Z.X. are partially supported by NIH R01HG006292 and R01HL129132 (awarded to Y. Li). Publisher Copyright: {\textcopyright} 2016 The Authors",
year = "2016",
month = nov,
day = "15",
doi = "10.1016/j.celrep.2016.10.061",
language = "English",
volume = "17",
pages = "2042--2059",
journal = "Cell Reports",
issn = "2211-1247",
number = "8",
}