Regulation of Immunoglobulin Class-Switch Recombination

Abstract

Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as “Ch genes”, e.g., Cγ, Cε, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.

Binding of AID to DNA Does Not Correlate with Mutator Activity

“…It is generally believed that transcribed S regions form R-loops, allowing AID to access S regions independent of its phosphorylation status (36). Phosphorylation of AID at S38 is still required to both promote formation of DSBs at S regions through interaction with APE1 (35), and for the repair of DSBs through recruitment of RPA to S regions (8, 23).…”

AID Recognizes Structured DNA for Class Switch Recombination

“…Deamination at both strands of DNA may contribute to double-strand breaks (DSBs) by co-opted repair pathways (Han et al, 2011; Yeap et al, 2015). Joining of AID-initiated DSBs replaces the IgM heavy chain constant region with that of other isotypes to achieve class switching (Matthews et al, 2014a). Patients with AID mutations produce mainly low-affinity IgM antibodies with impairment in CSR and/or SHM, a syndrome known as hyper-IgM immunodeficiency (Xu et al, 2012).…”

Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability

“…SHM occurs in germinal centers (GCs) of peripheral lymphoid tissues, where B cells are selected for mutations that generate BCRs with increased antigen affinity (Victora and Nussenzweig, 2012). IgH CSR involves generation and joining of IgH locus DSBs in switch (S) regions that precede various sets of IgH C H exons (“C H s”) to replace the initially expressed C H with a downstream C H , thereby, producing antibodies with different effector functions (Matthews et al, 2014). Both SHM and CSR are initiated by activation induced cytidine deaminase (AID) (Muramatsu et al, 2000), which deaminates cytosine to uridine on single-stranded DNA (ssDNA) (Di Noia and Neuberger, 2007).…”

“…In this regard, SHM of V(D)J exons in GC B cells begins about 150bp downstream of the transcription start site (TSS) and tapers off 1-2 kb downstream (Liu and Schatz, 2009). Likewise, each C H has a promoter upstream of the S region that upon induction by external signals generates transcription through the S region and, thereby, targets AID (Matthews et al, 2014). Mouse and human S regions also have a highly G-rich non-template strand that upon transcription forms stable R-loops that provide ssDNA to augment AID targeting (Matthews et al, 2014; Alt et al, 2013).…”