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Mol. Cell. Biol. doi:10.1128/MCB.00909-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Differential chromatin looping regulates CD4 expression in immature thymocytes

Departments of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, CA, 94143

^* To whom correspondence should be addressed. Email: matija.peterlin{at}ucsf.edu.

	Abstract

Runx1 binds the silencer and represses CD4 transcription in immature thymocytes. In this study, using looping-ChIP and 3C, we demonstrated that interactions between Runx1 and P-TEFb appose the silencer and enhancer in CD4-negative thymoma cells and double negative immature thymocytes. This chromatin loop decoys P-TEFb away from the promoter thus preventing RNA polymerase II from elongating on the CD4 gene. In the absence of Runx1 on the silencer, P-TEFb interacts with the transcription complex, forming a different chromatin loop between the enhancer and promoter, which leads to the expression of the CD4 gene in CD4-positive hybridoma cells and double positive thymocytes. Moreover, the knockdown of CycT1 from P-TEFb abolishes both of these chromatin loops. Finally, the selective removal and restoration of Runx1 causes rapid interchanges between these chromatin loops, which reveals the plasticity of this regulatory circuit. Thus, differential looping and decoying P-TEFb away from the promoter mediate active repression of the CD4 gene during thymocyte development.