What Targets Somatic Hypermutation to the Immunoglobulin Loci?

Abstract

One of the most profound enigmas in B cell biology is how activation-induced deaminase (AID) is targeted to a very small region of DNA in the immunoglobulin loci. Two specific regions are singled out: the variable region of 2 kb that contains rearranged genes on the heavy, κ light, and λ light chain loci, and the switch region of ∼4 kb that contains an extensive stretch of G:C rich DNA on the heavy chain locus. Transcription is required for AID recruitment; however, many genes are also highly transcribed and do not undergo the catastrophic mutagenesis that occurs in variable and switch regions. The DNA sequences of these regions cause RNA polymerase II to accumulate for an extended distance of 2-4 kb. The stalled polymerases then recruit the transcription cofactor Spt5, and AID, which deaminates cytosines to uracils in exposed transcription bubbles. Thus, the immunoglobulin loci are unique in that a favorable combination of DNA sequences and 3' transcription enhancers make them the perfect storm for AID-induced somatic hypermutation.

Keywords: AID; class switch recombination; somatic hypermutation; transcription.

FIG. 1.

Map of SHM in immunoglobulin loci. Mutation frequency is shown by the green arrow on the y-axis, and by green peaks centered over the VDJ and VJ exons and Sμ region. For V exons, mutation starts downstream of promoter (P) at the transcription start site (bent arrow) and L exon, and proceeds for ∼2 kb. For Sμ, mutation starts downstream of the intronic transcription start site (bent arrow), and proceeds for ∼4 kb. Exons are shown as purple rectangles, and Sμ is depicted by an orange oval. Intron enhancers (E) are shown as blue circles, and 3′ enhancers are designated by red circles and brackets. SHM, somatic hypermutation.

FIG. 2.

Secondary DNA structures promote AID activity in S regions. Transcription (bent arrow) starts in the intron E (blue). DNA sequences of the top nontranscribed strand and bottom transcribed strand are shown, with AGCT or TCGA hotspots shown in pink. As RNA polymerase II (red) transcribes through the S region, the transcript bonds with the C-rich transcribed DNA strand, creating an RNA-DNA hybrid or R-loop, and G quadruplexes form on the nontranscribed DNA strand. These structures slow transcription, and recruit AID (green). AID then deaminates C to U in hotspots on both strands. AID, activation-induced deaminase.

FIG. 3.

Correlation between RNA polymerase II, Spt5, AID, and SHM in V and S regions. RNA polymerase II is paused in the S region because of the G:C rich DNA sequence; however, it is not known why it is paused in the V region. RNA polymerase II, green line; AID, turquoise line; Spt5, solid red; and mutations, solid gold.