DNA Lesions and Repair in Immunoglobulin Class Switch Recombination and Somatic Hypermutation

Abstract

Immunoglobulin (Ig) gene somatic hypermutation (SHM) and class switch DNA recombination (CSR) are critical for the maturation of the antibody response. These processes endow antibodies with increased antigen-binding affinity and acquisition of new biological effector functions, thereby underlying the generation of memory B cells and plasma cells. They are dependent on the generation of specific DNA lesions and the intervention of activation-induced cytidine deaminase as well as newly identified translesion DNA polymerases, which are expressed in germinal center B cells. DNA lesions include mismatches, abasic sites, nicks, single-strand breaks, and doublestrand breaks (DSBs). DSBs in the switch (S) region DNA are critical for CSR, but they also occur in V(D)J regions and possibly contribute to the events that lead to SHM. The nature of the DSBs in the Ig locus, their generation, and the repair processes that they trigger and that are responsible for their regulation remain poorly understood. Aberrant regulation of these events can result in chromosomal breaks and translocations, which are significant steps in B-cell neoplastic transformation.Keywords activation-induced cytosine deaminase (AID); class switch recombination (CSR); DNA lesion; double-strand break (DSB); error-prone DNA repair; lesion bypass or translesion DNA polymerase; pol ι; pol θ; pol ζ; somatic hypermutation (SHM); V(D)J recombination

Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication

“…A similar increase in mitotic recombination and an additional elevation of spontaneous mutation rates in yeast has been associated with high levels of transcription carried out by RNA polymerase II [3][4][5][6][7]. The effect of such transcription-associated mutagenesis (TAM) and recombination (TAR) would be expected to be generally deleterious (e.g., the loss of a tumor suppressor), but may also be advantageous, promoting processes such as in immunoglobulin somatic hypermutation [8].…”

Mouse models of DNA polymerases

“…Polq 2/2 mice had anatomically normal spleens, Peyers patches and B cells. However, sequencing of the VDJ regions revealed that they had a greater than 60% decrease in mutations in antigen selected V186.2DJ H transcripts and a greater than 80% decrease in mutations in the Ig H chain of intronic J H 4-iEl sequence Xu et al, 2005]. These findings implicate Pol y in the process of somatic hypermutation.…”

“…DSBs can be repaired by nonhomologous end-joining (NHEJ) or homologous recombination (HR). The DNA polymerases Pol e, Pol b, Pol f, Pol h, Pol y, Pol k, Pol l function in DSB repair by HR or NHEJ [Holbeck et al, 1993;Jessberger et al, 1993;Wang et al, 2004;Xu et al, 2005;Zan et al, 2005;Rattray and Strathern, 2005;Masuda et al, 2006;Nick McElhinny, 2008;Kidane et al, 2010;Moldovan et al, 2010]. The pathways of homologous recombination and nonhomologous end-joining have been reviewed in Chaudhuri and Alt [2004] and San Filippo et al [2008].…”

Biased dA/dT somatic hypermutation as regulated by the heavy chain intronic iEμ enhancer and 3′Eα enhancers in human lymphoblastoid B cells

“…A dA/dT-biased targeting may involve DNA cleavage by a yet-to-be-defined endonuclease, perhaps encoded by an AIDedited mRNA ("RNA editing" hypothesis) (Honjo et al, 2002Doi et al, 2003;Begum et al, 2004;Nagaoka et al, 2005), and would entail the generation of resected DSBs. Such resected ends have been shown to preferentially target RGYW/WRCY motifs and are repaired by translesion DNA polymerases (Zan et al, 2001Xu et al, 2005).…”

“…However, mounting evidence indicates that AID directly deaminates DNA dC residues (Petersen-Mahrt et al, 2002;Pham et al, 2003), yielding dU:dG mispairs, which are replicated over or dealt with either the base excision repair (BER) or the mismatch repair (MMR) pathways to introduce mutations through the intervention of translesion DNA polymerases, such as pol ζ, pol η and pol θ (Rada et al, 2004). In addition, accumulating evidence suggests that mutations can be introduced by the same translesion DNA polymerases (Zan et al, 2001;Diaz and Casali, 2002;Diaz and Lawrence, 2005) while repairing DNA breaks, including double stranded DNA breaks (DSBs) involving resected ends generated through AID-dependent DNA deamination (Bross et al, 2000;Papavasiliou and Schatz, 2000;Wu et al, 2003;Zan et al, 2003;Nagaoka et al, 2005;Xu et al, 2005). SHM depends on V gene transcription (Peters and Storb, 1996;Fukita et al, 1998), as suggested by the greatly diminished frequency of mutations in the IgH locus when the V gene promoter is removed (Fukita et al, 1998), and conversely, by unchanged level of SHM in V regions if the endogenous promoter is replaced with a transcriptionally active heterologous promoter (Betz et al, 1994;).…”