title: Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region.
abstract: The mechanism by which the cytidine deaminase activation-induced deaminase (AID) acts at immunoglobulin heavy-chain class switch regions during mammalian class switch recombination (CSR) remains unclear. R-loops have been proposed as a basis for this targeting. Here, we show that the difference between various forms of the Smu locus that can or cannot undergo CSR correlates well with the locations and detectability of R-loops. The Smu R-loops can initiate hundreds of base pairs upstream of the core repeat switch regions, and the area where the R-loops initiate corresponds to the zone where the AID mutation frequency begins to rise, despite a constant density of WRC sites in this region. The frequency of R-loops is 1 in 25 alleles, regardless of the presence of the core Smu repeats, again consistent with the initiation of most R-loops upstream of the core repeats. These findings explain the surprisingly high levels of residual CSR in B cells from mice lacking the core Smu repeats but the marked reduction in CSR in mice with deletions of the region upstream of the core Smu repeats. These studies also provide the first analysis of how R-loop formation in the eukaryotic chromosome depends on the DNA sequence.
authors.affiliation: Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, California 90089-9176, USA.
authors.forename: Feng-Ting
authors.initials: FT
authors.lastname: Huang
authors.forename: Kefei
authors.initials: K
authors.lastname: Yu
authors.forename: Barbara B
authors.initials: BB
authors.lastname: Balter
authors.forename: Erik
authors.initials: E
authors.lastname: Selsing
authors.forename: Zeliha
authors.initials: Z
authors.lastname: Oruc
authors.forename: Ahmed Amine
authors.initials: AA
authors.lastname: Khamlichi
authors.forename: Chih-Lin
authors.initials: CL
authors.lastname: Hsieh
authors.forename: Michael R
authors.initials: MR
authors.lastname: Lieber
mesh_terms: D000483:Alleles; D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism; D001483:Base Sequence; D033481:Chromosomes, Mammalian / Q000737:chemistry / Q000235:genetics*; D007134:Immunoglobulin Switch Region / Q000235:genetics*; D007148:Immunoglobulin mu-Chains / Q000235:genetics*; D008213:Lymphocyte Activation; D051379:Mice; D008810:Mice, Inbred C57BL; D011995:Recombination, Genetic / Q000235:genetics; D016914:Ribonuclease H / Q000378:metabolism; D017384:Sequence Deletion
chemical_list: D007148:Immunoglobulin mu-Chains; D016914:Ribonuclease H