title: Interplay between Target Sequences and Repair Pathways Determines Distinct Outcomes of AID-Initiated Lesions.
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.
authors.affiliation: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and Department of Biomedical Research, National Jewish Health, Denver, CO 80206.
authors.forename: Zhangguo
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and.
authors.forename: Maxwell D
authors.initials: MD
authors.lastname: Eder
authors.affiliation: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and.
authors.forename: Mihret T
authors.initials: MT
authors.lastname: Elos
authors.affiliation: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and.
authors.forename: Sawanee S
authors.initials: SS
authors.lastname: Viboolsittiseri
authors.affiliation: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and.
authors.forename: Xiaomi
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and Department of Biomedical Research, National Jewish Health, Denver, CO 80206 jing.wang@ucdenver.edu.
authors.forename: Jing H
authors.initials: JH
authors.lastname: Wang
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D003564:Cytidine Deaminase / Q000378:metabolism*; D053843:DNA Mismatch Repair; D004260:DNA Repair; D055879:Gene Knock-In Techniques; D023061:Gene Order; D018390:Gene Targeting; D056426:Genetic Loci; D051379:Mice; D018345:Mice, Knockout; D051718:MutS Homolog 2 Protein / Q000378:metabolism; D009154:Mutation; D059645:Mutation Rate; D059372:Nucleotide Motifs; D013379:Substrate Specificity; D051981:Uracil-DNA Glycosidase / Q000378:metabolism; D050441:VDJ Exons / Q000235:genetics; D000098830:AICDA (Activation-Induced Cytidine Deaminase)
chemical_list: D051981:Uracil-DNA Glycosidase; D000098830:AICDA (Activation-Induced Cytidine Deaminase); D003564:Cytidine Deaminase; D051718:MutS Homolog 2 Protein
references.citation: J Exp Med. 2006 Sep 4;203(9):2085-94
references.pmid: 16894013
references.citation: J Exp Med. 1998 Aug 17;188(4):689-98
references.pmid: 9705951
references.citation: J Exp Med. 2007 Jan 22;204(1):7-10
references.pmid: 17190841
references.citation: Adv Immunol. 2007;94:157-214
references.pmid: 17560275
references.citation: Trends Immunol. 2009 Apr;30(4):173-81
references.pmid: 19303358
references.citation: J Exp Med. 2009 Jun 8;206(6):1237-44
references.pmid: 19433618
references.citation: J Immunol. 2009 Jul 15;183(2):1222-8
references.pmid: 19553545
references.citation: Nat Struct Mol Biol. 2010 Sep;17(9):1124-35
references.pmid: 20729863
references.citation: Trends Immunol. 2011 May;32(5):194-201
references.pmid: 21493144
references.citation: J Immunol. 2012 Apr 15;188(8):3559-66
references.pmid: 22492685
references.citation: J Exp Med. 2012 Jul 2;209(7):1379-89
references.pmid: 22665573
references.citation: Semin Immunol. 2012 Aug;24(4):293-300
references.pmid: 22703640
references.citation: J Immunol. 2012 Oct 15;189(8):3970-82
references.pmid: 22962683
references.citation: Genes Immun. 2012 Oct;13(7):523-9
references.pmid: 22717702
references.citation: Front Med. 2014 Jun;8(2):201-16
references.pmid: 24748462
references.citation: J Immunol. 2014 Dec 1;193(11):5545-56
references.pmid: 25339658
references.citation: Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):E728-37
references.pmid: 25646473
references.citation: J Immunol. 2015 Dec 1;195(11):5461-71
references.pmid: 26500350
references.citation: Cell. 2015 Nov 19;163(5):1124-37
references.pmid: 26582132
references.citation: Nat Immunol. 2004 Dec;5(12):1275-81
references.pmid: 15531884
references.citation: J Exp Med. 2006 Feb 20;203(2):319-23
references.pmid: 16476771
references.citation: Annu Rev Biochem. 2007;76:1-22
references.pmid: 17328676
references.citation: J Exp Med. 2007 Nov 26;204(12):3017-26
references.pmid: 18025127
references.citation: Nature. 2008 Feb 14;451(7180):841-5
references.pmid: 18273020
references.citation: Philos Trans R Soc Lond B Biol Sci. 2009 Mar 12;364(1517):645-52
references.pmid: 19010771
references.citation: Adv Immunol. 2009;101:163-89
references.pmid: 19231595
references.citation: Mutat Res. 2000 Aug 30;460(3-4):183-99
references.pmid: 10946228
references.citation: J Exp Med. 2001 Jan 15;193(2):159-68
references.pmid: 11148220
references.citation: Immunol Cell Biol. 2001 Feb;79(1):18-22
references.pmid: 11168618
references.citation: Curr Opin Immunol. 2001 Apr;13(2):208-18
references.pmid: 11228415
references.citation: Nat Immunol. 2001 Jun;2(6):530-6
references.pmid: 11376340
references.citation: Immunity. 2002 Jan;16(1):123-34
references.pmid: 11825571
references.citation: Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9984-9
references.pmid: 12114543
references.citation: Curr Biol. 2002 Oct 15;12(20):1748-55
references.pmid: 12401169
references.citation: J Exp Med. 2003 Jun 16;197(12):1767-78
references.pmid: 12810694
references.citation: Nature. 2003 Jul 3;424(6944):103-7
references.pmid: 12819663
references.citation: Immunity. 2003 Oct;19(4):515-24
references.pmid: 14563316
references.citation: Nat Rev Immunol. 2004 Jul;4(7):541-52
references.pmid: 15229473
references.citation: Nature. 2004 Aug 26;430(7003):992-8
references.pmid: 15273694
references.citation: Mol Cell. 2004 Oct 22;16(2):163-71
references.pmid: 15494304
references.citation: Cell. 1981 Jun;24(3):625-37
references.pmid: 6788376
references.citation: Eur J Immunol. 1992 Feb;22(2):511-7
references.pmid: 1537385
references.citation: Biochim Biophys Acta. 1992 Nov 15;1171(1):11-8
references.pmid: 1420357
references.citation: Biochem J. 1992 Nov 1;287 ( Pt 3):1007-10
references.pmid: 1359874
references.citation: Biochemistry. 1995 May 9;34(18):6109-19
references.pmid: 7742315
references.citation: Nature. 1995 Jul 20;376(6537):225-9
references.pmid: 7617031
references.citation: Nature. 1995 Aug 31;376(6543):732
references.pmid: 7651532
references.citation: Immunity. 1997 Mar;6(3):225-33
references.pmid: 9075923
references.citation: J Exp Med. 1998 Jan 5;187(1):59-70
references.pmid: 9419211
references.citation: J Immunol. 1998 Jul 15;161(2):782-90
references.pmid: 9670955
references.citation: Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8791-4
references.pmid: 9671757
references.citation: Immunity. 1998 Jul;9(1):105-14
references.pmid: 9697840
references.citation: Immunity. 1998 Jul;9(1):135-41
references.pmid: 9697843
references.citation: Eur J Immunol. 2007 Jan;37(1):235-9
references.pmid: 17183606