Open AccessCTCF-dependent enhancer-blocking by alternative chromatin loop formation
Author(s) -
Chunhui Hou,
Hui Zhao,
Koichi Tanimoto,
Ann Dean
Publication year - 2008
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.0808506106
Subject(s) - ctcf , chromatin , locus control region , enhancer , hypersensitive site , activator (genetics) , biology , dnase i hypersensitive site , microbiology and biotechnology , globin , gene , deoxyribonuclease i , genetics , gene expression , base sequence
The mechanism underlying enhancer-blocking by insulators is unclear. We explored the activity of human β-globin HS5, the orthologue of the CTCF-dependent chicken HS4 insulator. An extra copy of HS5 placed between the β-globin locus control region (LCR) and downstream genes on a transgene fulfills the classic predictions for an enhancer-blocker. Ectopic HS5 does not perturb the LCR but blocks gene activation by interfering with RNA pol II, activator and coactivator recruitment, and epigenetic modification at the downstream β-globin gene. Underlying these effects, ectopic HS5 disrupts chromatin loop formation between β-globin and the LCR, and instead forms a new loop with endogenous HS5 that topologically isolates the LCR. Both enhancer-blocking and insulator-loop formation depend on an intact CTCF site in ectopic HS5 and are sensitive to knock-down of the CTCF protein by siRNA. Thus, intrinsic looping activity of CTCF sites can nullify LCR function.