Abstract
The somatic hypermutation (SHM) of Immunoglobulin (Ig) genes is a key process during antibody affinity maturation in B cells. The mutagenic enzyme activation induced deaminase (AID) is required for SHM and has a preference for WRC hotspots in DNA. Error-prone repair mechanisms acting downstream of AID introduce further mutations, including DNA polymerase eta (Polη), part of the non-canonical mismatch repair pathway (ncMMR), which preferentially generates mutations at WA hotspots. Previously proposed mechanistic models lead to a variety of predictions concerning interactions between hotspots, for example, how mutations in one hotspot will affect another hotspot. Using a large, high-quality, Ig repertoire sequencing dataset, we evaluated pairwise correlations between mutations site-by-site using an unbiased measure similar to mutual information which we termed “mutational association” (MA). Interactions are dominated by relatively strong correlations between nearby sites (short-range MAs), which can be almost entirely explained by interactions between overlapping hotspots for AID and/or Polη. We also found relatively weak dependencies between almost all sites throughout each gene (longer-range MAs), although these arise mostly as a statistical consequence of high pairwise mutation frequencies. The dominant short-range interactions are also highest within the most highly mutating IGHV sub-regions, such as the complementarity determining regions (CDRs), where there is a high hotspot density. Our results suggest that the hotspot preferences for AID and Polη have themselves evolved to allow for greater interactions between AID and/or Polη induced mutations.
Highlights
The process of somatic hypermutation (SHM) is a key component of antibody affinity maturation in B cells
Because the mutation spectra of nonproductive sequences should be unaffected by selection, these results suggest that intrinsic bias is dominant in SHM with selection playing at most a minor role
To better explain the observed importance of short-range mutational association” (MA) and the relationship with hotspot interactions, we considered a generalized model of overlapping hotspots that took into account interactions between activation induced deaminase (AID) hotspots and considered Polh hotspots
Summary
The process of somatic hypermutation (SHM) is a key component of antibody affinity maturation in B cells. Activation induced deaminase (AID) initiates SHM by introducing C>U mutations in single-stranded DNA (ssDNA) at the antibody (Immunoglobulin or Ig) loci [reviewed in [1]]. These mutations are preferentially inserted at AID hotspots defined by the motif WRC (W = A/T, R = A/G), where the underline indicates the mutating nucleotide [2]. Polymerase eta (Polh), which is part of the ncMMR pathway, introduces mutations preferentially at hotspots defined by the motif WA [5]. Previous work has shown that where two AID hotspots are opposite each other on the two DNA strands, defined by the motif WGCW, mutations occur at a high frequency [6]. A recent study by ourselves found that colocalization of AID WGCW and Polh WA hotspots characterizes major differences between human IGHV germline genes [9]
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