Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
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Author(s)
Dowen, Jill M.
Fan, Zi Peng
Hnisz, Denes
Ren, Gang
Abraham, Brian J.
Weintraub, Abraham S.
Schuijers, Jurian
Lee, Tong Ihn
Zhao, Keji
Zhang, Lyndon Nuoxi
Date Issued
October 2014
Journal
Cell
Publisher
Elsevier
Citation
Dowen, Jill M. et al. “Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes.” Cell 159.2 (2014): 374–387.
Version
Author's final manuscript
Abstract
The pluripotent state of embryonic stem cells (ESCs) is produced by active transcription of genes that control cell identity and repression of genes encoding lineage-specifying developmental regulators. Here, we use ESC cohesin ChIA-PET data to identify the local chromosomal structures at both active and repressed genes across the genome. The results produce a map of enhancer-promoter interactions and reveal that super-enhancer-driven genes generally occur within chromosome structures that are formed by the looping of two interacting CTCF sites co-occupied by cohesin. These looped structures form insulated neighborhoods whose integrity is important for proper expression of local genes. We also find that repressed genes encoding lineage-specifying developmental regulators occur within insulated neighborhoods. These results provide insights into the relationship between transcriptional control of cell identity genes and control of local chromosome structure.
MIT Department
Massachusetts Institute of Technology. Department of Biology
Whitehead Institute for Biomedical Research
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Creative Commons Attribution-NonCommercial-NoDerivs License
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DOI of Published Version
https://doi.org/10.1016/j.cell.2014.09.030
