The strength of an Ig switch region is determined by its ability to drive R loop formation and its number of WGCW sites

Cell Rep. 2014 Jul 24;8(2):557-69. doi: 10.1016/j.celrep.2014.06.021. Epub 2014 Jul 10.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • B-Lymphocytes / metabolism
  • Cell Line, Tumor
  • GC Rich Sequence
  • Immunoglobulin Class Switching*
  • Immunoglobulin Switch Region*
  • Mice
  • Nucleic Acid Conformation