Figure 7. Model for senataxin (SETX) and RNase H2 in promoting efficient class switch recombination (CSR).

When B cells are stimulated to undergo class switching, PolII-mediated transcription opens duplex DNA at recombining S regions. R loops formed during transcription promote activation-induced cytidine deaminase (AID) binding to ssDNA on the non-template strand first. SETX and RNase H2 then cooperate to remove switch region R loops, exposing ssDNA on the template strand for AID to bind. Extensive AID activity and uracil removal on both strands results in the formation of double-stranded breaks (DSBs) with limited single-strand DNA (ssDNA) overhangs at break ends (‘blunted’ ends), which are predominantly repaired by classical non-homologous end joining (cNHEJ). When SETX and RNase H2B are absent, R loops forming at S region are not efficiently removed and error-prone EJ is increased. This persistent R loop/RNA:DNA hybrid may affect CSR in two ways. One possible mechanism for increased error-prone EJ is that persistent R loops reduce the extent of ssDNA available for AID binding specifically on the template strand, increasing ssDNA tail length at DSB ends. Alternatively, persistent RNA:DNA hybrids may alter DNA repair protein recruitment to DSB ends, impeding end processing and/or ligation. Both possibilities reduce NHEJ efficiency, but do not affect overall CSR levels as the majority of breaks with long ssDNA tails are repaired by error-prone EJ. However, a subset of breaks are not repaired, leading to persistent DSBs that manifest as chromosome breaks and translocations in mitotic spreads.