Interplay between Target Sequences and Repair Pathways Determines Distinct Outcomes of AID-Initiated Lesions

J Immunol. 2016 Mar 1;196(5):2335-47. doi: 10.4049/jimmunol.1502184. Epub 2016 Jan 25.

Abstract

Activation-induced deaminase (AID) functions by deaminating cytosines and causing U:G mismatches, a rate-limiting step of Ab gene diversification. However, precise mechanisms regulating AID deamination frequency remain incompletely understood. Moreover, it is not known whether different sequence contexts influence the preferential access of mismatch repair or uracil glycosylase (UNG) to AID-initiated U:G mismatches. In this study, we employed two knock-in models to directly compare the mutability of core Sμ and VDJ exon sequences and their ability to regulate AID deamination and subsequent repair process. We find that the switch (S) region is a much more efficient AID deamination target than the V region. Igh locus AID-initiated lesions are processed by error-free and error-prone repair. S region U:G mismatches are preferentially accessed by UNG, leading to more UNG-dependent deletions, enhanced by mismatch repair deficiency. V region mutation hotspots are largely determined by AID deamination. Recurrent and conserved S region motifs potentially function as spacers between AID deamination hotspots. We conclude that the pattern of mutation hotspots and DNA break generation is influenced by sequence-intrinsic properties, which regulate AID deamination and affect the preferential access of downstream repair. Our studies reveal an evolutionarily conserved role for substrate sequences in regulating Ab gene diversity and AID targeting specificity.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Base Sequence
  • Binding Sites*
  • Cytidine Deaminase / metabolism*
  • DNA Mismatch Repair
  • DNA Repair*
  • Gene Knock-In Techniques
  • Gene Order
  • Gene Targeting
  • Genetic Loci
  • Mice
  • Mice, Knockout
  • MutS Homolog 2 Protein / metabolism
  • Mutation
  • Mutation Rate
  • Nucleotide Motifs*
  • Substrate Specificity
  • Uracil-DNA Glycosidase / metabolism
  • VDJ Exons / genetics

Substances

  • Uracil-DNA Glycosidase
  • AICDA (activation-induced cytidine deaminase)
  • Cytidine Deaminase
  • MutS Homolog 2 Protein