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CTCF and cohesin cooperatively mediate the cell-type specific interchromatin interaction between Bcl11b and Arhgap6 loci

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Abstract

CCCTC-binding factor (CTCF) is a master organizer of genome spatial organization and plays an important role in mediating extensive chromatin interactions. Circular chromosome conformation capture (4C) is a high-throughput approach that allows genome-wide screening for unknown potential interaction partners. Using a conserved CTCF binding site on the Bcl11b locus as bait, an interaction partner at the Arhgap6 locus on a different chromosome was identified by 4C. Additional experiments verified that the interchromatin interaction between the Bcl11b and Arhgap6 loci was cell-type specific, which was cooperatively mediated by CTCF and cohesin. Functional analysis showed that the interchromatin interaction partners were repressing regulatory elements. These results indicate that interaction chromatin loops regulate the expression of the relevant genes.

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Abbreviations

CTCF:

CCCTC-binding factor

3C:

Chromosome conformation capture

4C:

Circular chromosome conformation capture

BCL11B:

B-cell lymphoma/leukemia 11B

ChIP:

Chromatin immunoprecipitation

3D DNA-FISH:

Three dimensional DNA fluorescence in situ hybridization

Q-PCR:

Quantitative PCR

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Acknowledgments

The project was supported by the National Natural Science Foundation of China (30871374, 31071119, 31030026), and the National Key Basis Research Program of China (973) (2009CB825602). We should appreciate Dr. Christopher Brooks (Bioscience Editing Solutions) for revising language.

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Authors and Affiliations

  1. State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China

    Licheng Ren, Zhong Yang & Xiaoning Wang

  2. Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China

    Licheng Ren, Minglei Shi, Yang Wang & Zhihu Zhao

  3. State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China

    Zhong Yang & Xiaoning Wang

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  1. Licheng Ren
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  2. Minglei Shi
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  3. Yang Wang
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  4. Zhong Yang
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  5. Xiaoning Wang
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  6. Zhihu Zhao
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Correspondence to Zhihu Zhao.

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Ren, L., Shi, M., Wang, Y. et al. CTCF and cohesin cooperatively mediate the cell-type specific interchromatin interaction between Bcl11b and Arhgap6 loci. Mol Cell Biochem 360, 243–251 (2012). https://doi.org/10.1007/s11010-011-1063-3

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  • DOI: https://doi.org/10.1007/s11010-011-1063-3

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