title: The strength of an Ig switch region is determined by its ability to drive R loop formation and its number of WGCW sites.
abstract: R loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R loop formation, and on the number of WGCW sites.
authors.affiliation: USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Zheng Z
authors.initials: ZZ
authors.lastname: Zhang
authors.affiliation: USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Pannunzio
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Han
authors.affiliation: USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Chih-Lin
authors.initials: CL
authors.lastname: Hsieh
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA. Electronic address: yuke@msu.edu.
authors.forename: Kefei
authors.initials: K
authors.lastname: Yu
authors.affiliation: USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA. Electronic address: lieber@usc.edu.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Lieber
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism; D045744:Cell Line, Tumor; D020862:GC Rich Sequence; D017578:Immunoglobulin Class Switching; D007134:Immunoglobulin Switch Region; D051379:Mice; D009690:Nucleic Acid Conformation