Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2003 Jul;23(4):235-46.
doi: 10.1023/a:1024571714867.

Immunoglobulin somatic hypermutation: double-strand DNA breaks, AID and error-prone DNA repair

Xiaoping Wu  1 , Junli Feng, Atsumasa Komori, Edmund C Kim, Hong Zan, Paolo Casali
Affiliations
Review

Immunoglobulin somatic hypermutation: double-strand DNA breaks, AID and error-prone DNA repair

Xiaoping Wu et al. J Clin Immunol. 2003 Jul.

Abstract

Somatic hypermutation (SHM) is critical for antibody affinity maturation and the generation of memory B cells. Somatic mutations consist mainly of single nucleotide changes with rare insertions and deletions. Such changes would be introduced during error-prone repair of lesions involving single-strand DNA breaks (SSBs) or, more likely, double-strand DNA breaks (DSBs), as DSBs occur exclusively in genes that have the potentials to undergo SHM. In the human, such genes include Ig V, BCL6, and c-MYC. In these germline genes, DSBs are blunt. In rearranged Ig V, BCL6, and translocated c-MYC genes, blunt DSBs are processed to yield resected DNA ends. This process is dependent on the expression of activation-induced cytidine deaminase (AID), which is selectively expressed upon CD40-signaling in hypermutating B cells. CD40-induced and AID-dependent free 5'- and 3'-staggered DNA ends critically channel the repair of DSBs through the homologous recombination (HR) repair pathway. During HR, the modulation of critical translesion DNA polymerases, as signaled by cross-linking of the B cell receptor (BCR) for antigen, leads to the insertions of mismatches, i.e., mutations. The nature of DSBs, the possible roles of AID in the modification of DSBs and that of the translesion DNA polymerases zeta and iota in the subsequent repair process that lead to the insertions of mutations are discussed here within the context of an integrated model of SHM.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
AID-independent and AID-dependent stages of B cell differentiation. Schematic diagram shows the Ig H chain locus. Rectangles and ovals represent V or C exons and switch regions. In the bone marrow, RAG-dependent V(D)J recombination selects one of each of the V, D, and J segments from respective gene pools and combines them into a single V(D)J exon (AID-independent and RAG-dependent stage of B cell differentiation). In peripheral lymphoid organs, the BCR is further diversified by SHM in an AID-dependent and RAG-independent fashion. SHM introduces mutations in the rearranged VDJ exon, yielding B cell submutants with diversified antigen specificities from which high affinity immunoglobulin producers are selected. CSR substitutes the upstream Cμ region with a downstream CH region by deletion of the DNA intervening between Sμ and the downstream S region 5′ of the target C region. Deleted DNA is released as a “switch circle.” Like SHM, CSR is AID-dependent and RAG-independent.
Fig. 2
Fig. 2
The requirement for induction for SHM. BCR cross-linking and T cell contact through CD40:CD40L and CD86/CD80:CD28 coengagement are required for induction of SHM. AID, which is upregulated by CD40-signaling, could directly introduce mutations by DNA deamination or could edit mRNA for an exonuclease and/or endonuclease to modify the blunt DSB into the resected DSB. These are crucial to initiate DNA repair process that leads to SHM. BCR engagement upregulates translesion DNA polymerase ζ, which, together with other error-prone DNA polymerases, such as polymerase ι, is recruited to the repair pathway and inserts mutations.
Fig. 3
Fig. 3
(A) Point-mutations and blunt DSBs target the same residues in the rearranged VHDJH gene segment expressed in human CL-01 B cells. Letters above the VHDJH sequence depict base changes; wedges below the VHDJH sequence indicate positions of DSBs. RGYW/WRCY are highlighted in purple and RGY/RCY in green. (B) Most DSBs in rearranged VHDJH genes target the mutational RGY(W)/WRC(Y) hotspot. DSBs within RGY(W)/WRC(Y) and those outside are 69, 18, and 13%, respectively of the total blunt DSBs.
Fig. 4
Fig. 4
DNA polymerase ζ is regulated by BCR-signaling and plays a critical role in SHM, likely in concert with polymerase ι and concomitant with profound downregulation of polymerase η, as induced by BCR-signaling. Translesion DNA polymerase ι, polymerase η, and polymerase ζ are depicted in purple, yellow, and turquoise, respectively. The low processivity of polymerase η allows for extrinsic exonucleases to proofread the mismatched nucleotides it inserts. This together with the inability of polymerase η to elongate a DNA strand after incorporating the incorrect nucleotide opposite a lesion allows this polymerase to perform error-free translesion synthesis of damaged DNA. Polymerase ζ efficiently extends damaged DNA, in concert with the error-prone, low processivity polymerase ι, after the incorporation of one or two mismatched deoxynucleotides by this polymerase. Polymerase ι and polymerase ζ act sequentially: polymerase ι as a “mispair inserter” and polymerase ζ as “mispair extender,” and this lesion-bypass DNA synthesis is continued by polymerase δ and polymerase ε. BCR cross-linking also signals the upregulation of DNA polymerase ζ, thereby allowing for the mismatches inserted by polymerase ι to be efficiently extended, giving rise to a newly synthesized DNA strand containing point-mutations.
Fig. 5
Fig. 5
An integrated model for SHM. DSBs target V(D)J, BCL6, and c-MYC genes and initiate the process that leads to the introduction of somatic mutations through error-prone repair. In germline V and c-MYC genes of hypermutating or nonhyper-mutating B cells and in BCL6 of nonhypermutating B cells, DSBs are blunt and are repaired through NHEJ in a faultless fashion (a). In hypermutating rearranged V(D)J genes or germline BCL6 or c-MYC translocated into the Ig locus, blunt DSBs are either similarly resolved (a) or are modified in a CD40-induced and AID-dependent fashion to yield 5′- and 3′-protruding DNA ends. Other resected DSBs may also be generated as such. Generation of resected DSBs as such or through modification of blunt DSBs would occur through intervention of an AID-edited endonuclease and/or exonuclease or direct AID-dependent deamination. 3′-Recessed termini may be filled in by an error-free DNA polymerase (in absence of BCR cross-linking) (b) or by an error-prone DNA polymerase (upon BCR cross-linking) with introduction of mismatches (c), and then resolved by NHEJ. 3′-Protruding ends can invade sister chromatid strands and initiate a HR process which, upon BCR cross-linking, involves the activity of the translesion DNA polymerase ζ. Polymerase ζ, possibly in concern with polymerase ι, extends DNA strands past mispair, eventually leading to SHM (d). In the absence of BCR cross-linking, HR proceeds in an error-free fashion (e). DSBs do not target C regions and no mutations can be introduced in this DNA (f)
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Pascual V, Liu YL, Magalski A, de Bouteiller O, Banchereau J, Capra JD. Analysis of somatic mutation in five B cell subsets of human tonsil. J Exp Med. 1994;180:329–339. - PMC - PubMed
    1. Pulendran B, Kannourakis G, Nouri S, Smith KG, Nossal GJ. Soluble antigen can cause enhanced apoptosis of germinal-centre B cells. Nature. 1995;375:331–334. - PubMed
    1. Cornall RJ, Goodnow CC, Cyster JG. The regulation of self-reactive B cells. Curr Opin Immunol. 1995;7:804–811. - PubMed
    1. Hertz M, Nemazee D. Receptor editing and commitment in B lymphocytes. Curr Opin Immunol. 1998;10:208–213. - PubMed
    1. Miller C, Stedra J, Kelsoe G, Cerny J. Facultative role of germinal centers and T cells in the somatic diversification of IgVH genes. J Exp Med. 1995;181:1319–1331. - PMC - PubMed

Publication types