As class switch recombination (CSR) is a region, rather than a site-specific event, a relationship between the recombination breakpoints and the structural character of the switch (S) regions involved has been sought. It has earlier been suggested that CSR preferentially occurs at transitions from a stem to a loop structure in ssDNA (microsites) in S regions from a variety of species (1, 2). However, only a limited number of breakpoints have been analyzed (1, 2). In the October 1, 2003 issue of The Journal of Immunology, Cameron et al. (3) showed that three of the four breakpoints described (Sμ, Sε, and Sγ) from nasal tissue also mapped to microsites and suggested that their observations represented the first evidence for a structural recognition pattern in primary human B cells. However, we have previously shown, using a large number of Sγ breakpoints from in vivo switched human B cells, that the percentage of breakpoints at microsites is not higher than expected by chance (4). We have now reanalyzed our previously published Sγ breakpoints (n = 68) and added another 130 Sμ and 62 Sα breakpoints, using the standard applied by Tashiro et al. (2). As shown in Table I, the percentage of breakpoints at microsites is not higher than expected by chance (χ2 test), even though many S junctions are indeed located at (position 0), or in the proximity of (position 1), these sites (for full data see www.biosci.ki.se/users/qipa/microsites). Therefore, new ways of exploring the role of secondary and tertiary structure of the S regions are required to explain the location of the switch recombination breakpoints.

Table I.

Occurrence of breakpoints in the proximity of the transitions from stem-to-loop regions in the secondary structure (microsites) in human S regionsa

S RegionDistance from Microsites (nucleotides)
00 or 1
Expected (%)ObservedExpected (%)Observed
Sμ 69 67% (87/130) 90 85% (110/130) 
Sγ 44 36% (24/67) 67 69% (46/67) 
Sα 55 53% (33/62) 77 68% (42/62) 
S RegionDistance from Microsites (nucleotides)
00 or 1
Expected (%)ObservedExpected (%)Observed
Sμ 69 67% (87/130) 90 85% (110/130) 
Sγ 44 36% (24/67) 67 69% (46/67) 
Sα 55 53% (33/62) 77 68% (42/62) 
a

Fragments of 200 bp of the Sμ, Sγ, or Sα regions were folded in regions spanning the switch recombination breakpoints, using the Mfold program developed by M. Zuker (http://mfold.burnet.edu.au/). The structure with the lowest free energy of duplex formation was chosen for analysis. When microhomology at the switch junction was observed, the 3′ nucleotide of the upstream breakpoint (Sμ) and the 5′ nucleotide of the downstream breakpoint (Sγ or Sα) were analyzed. The Sγ breakpoints include 42 Sγ3 and 26 Sγ4 breakpoints, and the Sα breakpoints include 42 Sα1 and 20 Sα2 breakpoints.

1
Mussmann, R., M. Courtet, J. Schwager, L. Du Pasquier.
1997
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Tashiro, J., K. Kinoshita, T. Honjo.
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3
Cameron, L., A. S. Gounni, S. Frenkiel, F. Lavigne, D. Vercelli, Q. Hamid.
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. SεSμ and SεSγ switch circles in human nasal mucosa following ex vivo allergen challenge: evidence for direct as well as sequential class switch recombination.
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Pan, Q., L. Hammarström.
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