title: Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding.
abstract: CTCF-mediated chromatin interactions influence organization and function of mammalian genome in diverse ways. We analyzed the interactions among CTCF binding sites (CBS) at the murine TCRb locus to discern the role of CTCF-mediated interactions in the regulation of transcription and VDJ recombination. Chromosome conformation capture analysis revealed thymocyte-specific long-range intrachromosomal interactions among various CBS across the locus that were relevant for defining the limit of the enhancer Eb-regulated recombination center (RC) and for facilitating the spatial proximity of TCRb variable (V) gene segments to the RC. Ectopic CTCF binding in the RC region, effected via genetic manipulation, altered CBS-directed chromatin loops, interfered with RC establishment, and reduced the spatial proximity of the RC with Trbv segments. Changes in chromatin loop organization by ectopic CTCF binding were relatively modest but influenced transcription and VDJ recombination dramatically. Besides revealing the importance of CTCF-mediated chromatin organization for TCRb regulation, the observed chromatin loops were consistent with the emerging idea that CBS orientations influence chromatin loop organization and underscored the importance of CBS orientations for defining chromatin architecture that supports VDJ recombination. Further, our study suggests that in addition to mediating long-range chromatin interactions, CTCF influences intricate configuration of chromatin loops that govern functional interactions between elements.
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Pratishtha
authors.initials: P
authors.lastname: Rawat
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Manisha
authors.initials: M
authors.lastname: Jalan
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Ananya
authors.initials: A
authors.lastname: Sadhu
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Abhilasha
authors.initials: A
authors.lastname: Kanaujia
authors.affiliation: National Institute of Immunology, New Delhi, India madhus@nii.res.in.
authors.forename: Madhulika
authors.identifier: http://orcid.org/0000-0002-0997-013X
authors.initials: M
authors.lastname: Srivastava
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000276:immunology; D000076246:CCCTC-Binding Factor; D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics; D016678:Genome / Q000235:genetics; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D060152:V(D)J Recombination / Q000235:genetics*
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; C000619698:Ctcf protein, mouse; D016693:Receptors, Antigen, T-Cell, alpha-beta; D012097:Repressor Proteins
keywords: CTCF; VDJ recombination; antigen receptor loci; chromatin loop; chromatin organization