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Cell. 2015 Aug 13;162(4):900-10. doi: 10.1016/j.cell.2015.07.038.

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Author information

1
Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China.
2
Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168(th) Street, New York, NY 10032, USA.
3
Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
4
Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA; MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
5
Cold Spring Harbor Laboratory, 1 Bungtown Rd, NY 11724, USA.
6
Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168(th) Street, New York, NY 10032, USA. Electronic address: tm2472@cumc.columbia.edu.
7
Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China. Electronic address: qwu123@gmail.com.

Abstract

CTCF and the associated cohesin complex play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context, the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. These findings reveal how 3D chromosome architecture can be encoded by linear genome sequences.

PMID:
26276636
PMCID:
PMC4642453
DOI:
10.1016/j.cell.2015.07.038
[Indexed for MEDLINE]
Free PMC Article

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