IgH class switching and translocations use a robust non-classical end-joining pathway

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Abstract
Programmed DNA breaks are made and repaired at two points during the development of antibody-producing B cells. While the breaks occurring during V(D)J recombination utilize factors that promote non-homologous end joining, this study finds that breaks that happen during class switch recombination require only a subset of these factors, suggesting that there are other as-yet-unrecognized proteins that function in this process. Immunoglobulin variable region exons are assembled in developing B cells by V(D)J recombination. Once mature, these cells undergo class-switch recombination (CSR) when activated by antigen. CSR changes the heavy chain constant region exons (Ch) expressed with a given variable region exon from Cμ to a downstream Ch (for example, Cγ, Cε or Cα), thereby switching expression from IgM to IgG, IgE or IgA. Both V(D)J recombination and CSR involve the introduction of DNA double-strand breaks and their repair by means of end joining1,2. For CSR, double-strand breaks are introduced into switch regions that flank Cμ and a downstream Ch, followed by fusion of the broken switch regions1. In mammalian cells, the ‘classical’ non-homologous end joining (C-NHEJ) pathway repairs both general DNA double-strand breaks and programmed double-strand breaks generated by V(D)J recombination2,3. C-NHEJ, as observed during V(D)J recombination, joins ends that lack homology to form ‘direct’ joins, and also joins ends with several base-pair homologies to form microhomology joins3,4. CSR joins also display direct and microhomology joins, and CSR has been suggested to use C-NHEJ5,6,7,8. Xrcc4 and DNA ligase IV (Lig4), which cooperatively catalyse the ligation step of C-NHEJ, are the most specific C-NHEJ factors; they are absolutely required for V(D)J recombination and have no known functions other than C-NHEJ2. Here we assess whether C-NHEJ is also critical for CSR by assaying CSR in Xrcc4- or Lig4-deficient mouse B cells. C-NHEJ indeed catalyses CSR joins, because C-NHEJ-deficient B cells had decreased CSR and substantial levels of IgH locus (immunoglobulin heavy chain, encoded by Igh) chromosomal breaks. However, an alternative end-joining pathway, which is markedly biased towards microhomology joins, supports CSR at unexpectedly robust levels in C-NHEJ-deficient B cells. In the absence of C-NHEJ, this alternative end-joining pathway also frequently joins Igh locus breaks to other chromosomes to generate translocations.