Molecular and Cellular Biochemistry

, Volume 360, Issue 1, pp 243–251

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

  • Licheng Ren
  • Minglei Shi
  • Yang Wang
  • Zhong Yang
  • Xiaoning Wang
  • Zhihu Zhao
Article

DOI: 10.1007/s11010-011-1063-3

Cite this article as:
Ren, L., Shi, M., Wang, Y. et al. Mol Cell Biochem (2012) 360: 243. doi:10.1007/s11010-011-1063-3

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.

Keywords

CCCTC-binding factor Chromosome conformation capture Circular chromosome conformation capture Interchromatin interaction B-cell lymphoma/leukemia 11B 

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

Supplementary material

11010_2011_1063_MOESM1_ESM.doc (30 kb)
Supplementary material 1 (DOC 30 kb)

Copyright information

© Springer Science+Business Media, LLC. 2011

Authors and Affiliations

  • Licheng Ren
    • 1
    • 2
  • Minglei Shi
    • 2
  • Yang Wang
    • 2
  • Zhong Yang
    • 1
    • 3
  • Xiaoning Wang
    • 1
    • 3
  • Zhihu Zhao
    • 2
  1. 1.State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiChina
  2. 2.Beijing Institute of BiotechnologyBeijingChina
  3. 3.State Key Laboratory of Genetic EngineeringSchool of Life Sciences, Fudan UniversityShanghaiChina