title: Constraints contributed by chromatin looping limit recombination targeting during Ig class switch recombination.
abstract: Engagement of promoters with distal elements in long-range looping interactions has been implicated in regulation of Ig class switch recombination (CSR). The principles determining the spatial and regulatory relationships among Igh transcriptional elements remain poorly defined. We examined the chromosome conformation of C region (CH) loci that are targeted for CSR in a cytokine-dependent fashion in mature B lymphocytes. Germline transcription (GLT) of the γ1 and ε CH loci is controlled by two transcription factors, IL-4-inducible STAT6 and LPS-activated NF-κB. We showed that although STAT6 deficiency triggered loss of GLT, deletion of NF-κB p50 abolished both GLT and γ1 locus:enhancer looping. Thus, chromatin looping between CH loci and Igh enhancers is independent of GLT production and STAT6, whereas the establishment and maintenance of these chromatin contacts requires NF-κB p50. Comparative analysis of the endogenous γ1 locus and a knock-in heterologous promoter in mice identified the promoter per se as the interactive looping element and showed that transcription elongation is dispensable for promoter/enhancer interactions. Interposition of the LPS-responsive heterologous promoter between the LPS-inducible γ3 and γ2b loci altered GLT expression and essentially abolished direct IgG2b switching while maintaining a sequential μ→γ3→γ2b format. Our study provides evidence that promoter/enhancer looping interactions can introduce negative constraints on distal promoters and affect their ability to engage in germline transcription and determine CSR targeting.
authors.affiliation: Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and.
authors.forename: Scott
authors.initials: S
authors.lastname: Feldman
authors.affiliation: Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and.
authors.forename: Ikbel
authors.initials: I
authors.lastname: Achour
authors.affiliation: Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and.
authors.forename: Robert
authors.initials: R
authors.lastname: Wuerffel
authors.affiliation: Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and.
authors.forename: Satyendra
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Gene Regulation Section, Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Gerasimova
authors.affiliation: Gene Regulation Section, Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, Baltimore, MD 21224.
authors.forename: Ranjan
authors.initials: R
authors.lastname: Sen
authors.affiliation: Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612; and star1@uic.edu.
authors.forename: Amy L
authors.initials: AL
authors.lastname: Kenter
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000166:cytology / Q000187:drug effects / Q000276:immunology*; D002843:Chromatin / Q000737:chemistry* / Q000276:immunology; D033481:Chromosomes, Mammalian; D005786:Gene Expression Regulation / Q000276:immunology; D056426:Genetic Loci; D017578:Immunoglobulin Class Switching / Q000235:genetics*; D007136:Immunoglobulins / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D015847:Interleukin-4 / Q000235:genetics / Q000276:immunology; D008070:Lipopolysaccharides / Q000494:pharmacology; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D016328:NF-kappa B / Q000172:deficiency / Q000235:genetics / Q000276:immunology; D011401:Promoter Regions, Genetic; D050800:STAT6 Transcription Factor / Q000172:deficiency / Q000235:genetics / Q000276:immunology; D015398:Signal Transduction; D013154:Spleen / Q000166:cytology / Q000187:drug effects / Q000276:immunology; D061805:Transcription Elongation, Genetic; D060152:V(D)J Recombination / Q000235:genetics*
chemical_list: D002843:Chromatin; D007136:Immunoglobulins; D008070:Lipopolysaccharides; D016328:NF-kappa B; D050800:STAT6 Transcription Factor; C494100:Stat6 protein, mouse; D015847:Interleukin-4