AIDing Chromatin and Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination

Abstract

Secondary diversification of the antibody repertoire upon antigenic challenge, in the form of immunoglobulin heavy chain (IgH) class-switch recombination (CSR) endows mature, naïve B cells in peripheral lymphoid organs with a limitless ability to mount an optimal humoral immune response, thus expediting pathogen elimination. CSR replaces the default constant (CH) region exons (Cμ) of IgH with any of the downstream CH exons (Cγ, Cε, or Cα), thereby altering effector functions of the antibody molecule. This process depends on, and is orchestrated by, activation-induced deaminase (AID), a DNA cytidine deaminase that acts on single-stranded DNA exposed during transcription of switch (S) region sequences at the IgH locus. DNA lesions thus generated are processed by components of several general DNA repair pathways to drive CSR. Given that AID can instigate DNA lesions and genomic instability, stringent checks are imposed that constrain and restrict its mutagenic potential. In this review, we will discuss how AID expression and substrate specificity and activity is rigorously enforced at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and how the DNA-damage response is choreographed with precision to permit targeted activity while limiting bystander catastrophe.

Elucidation of IgH 3′ region regulatory role during class switch recombination via germline deletion

“…Before the occurrence of DSBs, CSR is initiated by AID and the initial outcome of AID targeting can be the occurrence of base substitutions following cytidine deamination 12,14,15,21 . To gain an insight into this initial targeting, we analysed mutations in S regions and observed that both the S m donor and S g1 acceptor regions are less targeted by AID during IgG 1 CSR in 3 0 RR-deficient mice as compared with wt animals (Fig.…”

“…3a). A crucial step of CSR is the processing of AID lesions into DSBs, as a specific feature of S regions 14,15 . Ligation-mediated PCR (LM-PCR, see Supplementary Fig.…”

“…This shows that the 3 0 RR does not promote CSR only by fostering germline transcription. Transcription through S regions generates R loops in which the RNA stably hybridizes to the template strands, displacing the non-template strand as ssDNA 14,15 . For R loops experiments (see Supplementary Fig.…”

“…1a). CSR is a complex process involving epigenetic histone modifications for transcriptional accessibility, germline transcription, pausing of RNA Pol II, R loop formation, AID recruitment, AID-induced DNA double-strand breaks (DSBs) and their repair by means of end joining [11][12][13][14][15] . CSR uses the classical non-homologous end joining (C-NHEJ) pathway that predominantly joins ends that lack homology (direct joints).…”

APOBEC3 genes: retroviral restriction factors to cancer drivers

“…Alternatively, this strand bias is reminiscent of transcription-coupled AID mutagenesis, which acts upon structures called R-loops, in which the non-coding strand is selectively looped out and deaminated while the coding strand is hybridized to the primary transcript and thus protected [71].…”