The Journal of Experimental Medicine
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Published online March 17, 2008
doi:10.1084/jem.20071843
The Journal of Experimental Medicine, Vol. 205, No. 4, 785-798
The Rockefeller University Press, 0022-1007 $30.00
© 2008 Majumder et al.
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ARTICLE

 The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions

Parimal Majumder1, Jorge A. Gomez1, Brian P. Chadwick2, and Jeremy M. Boss1

1 Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
2 Institute for Genome Sciences and Policy, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710

CORRESPONDENCE Jeremy M. Boss: boss{at}microbio.emory.edu

Knockdown of the insulator factor CCCTC binding factor (CTCF), which binds XL9, an intergenic element located between HLA-DRB1 and HLA-DQA1, was found to diminish expression of these genes. The mechanism involved interactions between CTCF and class II transactivator (CIITA), the master regulator of major histocompatibility complex class II (MHC-II) gene expression, and the formation of long-distance chromatin loops between XL9 and the proximal promoter regions of these MHC-II genes. The interactions were inducible and dependent on the activity of CIITA, regulatory factor X, and CTCF. RNA fluorescence in situ hybridizations show that both genes can be expressed simultaneously from the same chromosome. Collectively, the results suggest a model whereby both HLA-DRB1 and HLA-DQA1 loci can interact simultaneously with XL9, and describe a new regulatory mechanism for these MHC-II genes involving the alteration of the general chromatin conformation of the region and their regulation by CTCF.

Abbreviations used: 3C, chromatin conformation capture; BAC, bacterial artificial chromosome; ChIP, chromatin immunoprecipitation assay; CIITA, class II transactivator; CREB, cAMP response element binding protein; CTCF, CCCTC binding factor; FISH, fluorescence in situ hybridization; MHC-II, MHC class II; NF-Y, nuclear factor–Y; RFX, regulatory factor X; siRNA, small interfering RNA.


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