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  • The EMBO Journal (2000) 19, 1055 - 1067
  • doi:10.1093/emboj/19.5.1055



There is a Retraction (September 2000) associated with this Article.

Transcription-dependent R-loop formation at mammalian class switch sequences

Robert B. Tracy1 and Michael R. Lieber1,2,3

  1. Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90089-9176, USA
  2. Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90089-9176, USA
  3. Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90089-9176, USA

Correspondence to:

Michael R. Lieber, E-mail: lieber@hsc.usc.edu

Received 8 November 1999; Accepted 12 January 2000; Revised 21 December 1999

Immunoglobulin class switching is mediated by recombination between switch sequences located immediately upstream of the immunoglobulin constant heavy chain genes. Targeting of recombination to particular switch sequences is associated temporally with transcription through these regions. We recently have provided evidence for inducible and stable RNA–DNA hybrid formation at switch sequences in the mouse genome that are mechanistically important for class switching in vivo. Here, we define in vitro the precise configuration of the DNA and RNA strands within this hybrid structure at the Smu, Sgamma3 and Sgamma2b mouse switch sequences. We find that the G-rich (non-template) DNA strand of each switch sequence is hypersensitive to probes throughout much of its length, while the C-rich (template) DNA strand is essentially resistant. These results demonstrate formation of an R-loop, whereby the G-rich RNA strand forms a stable heteroduplex with its C-rich DNA strand counterpart, and the G-rich DNA strand exists primarily in a single-stranded state. We propose that the organized structure of the R-loop is essential for targeting the class switch recombination machinery to these sequences.

  • Keywords:

    • class switch recombination,
    • DNA gyrase,
    • R-loop,
    • transcription