Antibody diversification necessitates targeted mutation of regions within the immunoglobulin locus by activation-induced cytidine deaminase (AID). While AID is known to act on single-stranded DNA (ssDNA), the source, structure, and distribution of these substrates in vivo remain unclear. Using the technique of in situ bisulfite treatment, we characterized these substrates—which we found to be unique to actively transcribed genes—as short ssDNA regions, that are equally distributed on both DNA strands. We found that the frequencies of these ssDNA patches act as accurate predictors of AID activity at reporter genes in hypermutating and class switching B cells as well as in Escherichia coli. Importantly, these ssDNA patches rely on transcription, and we report that transcription-induced negative supercoiling enhances both ssDNA tract formation and AID mutagenesis. In addition, RNaseH1 expression does not impact the formation of these ssDNA tracts indicating that these structures are distinct from R-loops. These data emphasize the notion that these transcription-generated ssDNA tracts are one of many in vivo substrates for AID.
Vyšlo v časopise: Negative Supercoiling Creates Single-Stranded Patches of DNA That Are Substrates for AID–Mediated Mutagenesis. PLoS Genet 8(2): e32767. doi:10.1371/journal.pgen.1002518 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002518
1. DurandyAHonjoT 2001 Human genetic defects in class-switch recombination (hyper-IgM syndromes). Curr Opin Immunol 13 543 548
2. Di NoiaJMNeubergerMS 2007 Molecular mechanisms of antibody somatic hypermutation. Annu Rev Biochem 76 1 22
3. PavriRGazumyanAJankovicMDi VirgilioMKleinI 2010 Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5. Cell 143 122 133
4. BasuUMengFLKeimCGrinsteinVPefanisE 2011 The RNA Exosome Targets the AID Cytidine Deaminase to Both Strands of Transcribed Duplex DNA Substrates. Cell 144 353 363
5. PetersAStorbU 1996 Somatic hypermutation of immunoglobulin genes is linked to transcription initiation. Immunity 4 57 65
6. BachlJCarlsonCGray-SchopferVDessingMOlssonC 2001 Increased transcription levels induce higher mutation rates in a hypermutating cell line. J Immunol 166 5051 5057
7. RamiroARStavropoulosPJankovicMNussenzweigMC 2003 Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand. Nat Immunol 4 452 456
8. DuquetteMLPhamPGoodmanMFMaizelsN 2005 AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation. Oncogene
9. Gomez-GonzalezBAguileraA 2007 Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex. Proc Natl Acad Sci U S A 104 8409 8414
10. RadaCDi NoiaJMNeubergerMS 2004 Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation. Mol Cell 16 163 171
11. FriederDLarijaniMCollinsCShulmanMMartinA 2009 The concerted action of Msh2 and UNG stimulates somatic hypermutation at A. T base pairs. Mol Cell Biol 29 5148 5157
12. MaulRWSaribasakHMartomoSAMcClureRLYangW 2011 Uracil residues dependent on the deaminase AID in immunoglobulin gene variable and switch regions. Nat Immunol 12 70 76
13. StavnezerJGuikemaJESchraderCE 2008 Mechanism and regulation of class switch recombination. Annu Rev Immunol 26 261 292
14. Petersen-MahrtSKHarrisRSNeubergerMS 2002 AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418 99 104
15. BransteitterRPhamPScharffMDGoodmanMF 2003 Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc Natl Acad Sci U S A 100 4102 4107
16. SohailAKlapaczJSamaranayakeMUllahABhagwatAS 2003 Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations. Nucleic Acids Res 31 2990 2994
17. LarijaniMMartinA 2007 Single-stranded DNA structure and positional context of the target cytidine determine the enzymatic efficiency of AID. Mol Cell Biol 27 8038 8048
18. RonaiDIglesias-UsselMDFanMLiZMartinA 2007 Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation. J Exp Med 204 181 190
19. KettenbergerHArmacheKJCramerP 2004 Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 16 955 965
20. AndreckaJTreutleinBArcusaMAMuschielokALewisR 2009 Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res 37 5803 5809
21. Martinez-RucoboFWSainsburySCheungACCramerP 2011 Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. Embo J 30 1302 1310
22. KleinBJBoseDBakerKJYusoffZMZhangX 2011 RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci U S A 108 546 550
23. ZhaoYDunn-WaltersDKBaroneFSpencerJ 2009 Antisense transcripts of V(D)J rearrangements; artifacts caused by false priming? Mol Immunol 46 2357 2362
24. YuKChedinFHsiehCLWilsonTELieberMR 2003 R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat Immunol 4 442 451
25. VallurACMaizelsN 2008 Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions. Proc Natl Acad Sci U S A 105 16508 16512
26. ShenHMStorbU 2004 Activation-induced cytidine deaminase (AID) can target both DNA strands when the DNA is supercoiled. Proc Natl Acad Sci U S A 101 12997 13002
27. WangCLHarperRAWablM 2004 Genome-wide somatic hypermutation. Proc Natl Acad Sci U S A 101 7352 7356
28. ZhangWBardwellPDWooCJPoltoratskyVScharffMD 2001 Clonal instability of V region hypermutation in the Ramos Burkitt's lymphoma cell line. Int Immunol 13 1175 1184
29. YangSYFugmannSDSchatzDG 2006 Control of gene conversion and somatic hypermutation by immunoglobulin promoter and enhancer sequences. J Exp Med 203 2919 2928
30. HuangFTYuKBalterBBSelsingEOrucZ 2007 Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region. Mol Cell Biol 27 5921 5932
31. ChenXKinoshitaKHonjoT 2001 Variable deletion and duplication at recombination junction ends: implication for staggered double-strand cleavage in class-switch recombination. Proc Natl Acad Sci U S A 98 13860 13865
32. MartinAScharffMD 2002 AID and mismatch repair in antibody diversification. Nature Rev Immunol 2 605 614
33. RushJSFugmannSDSchatzDG 2004 Staggered AID-dependent DNA double strand breaks are the predominant DNA lesions targeted to S mu in Ig class switch recombination. Int Immunol 16 549 557
34. Reina-San-MartinBDifilippantonioSHanitschLMasilamaniRFNussenzweigA 2003 H2AX is required for recombination between immunoglobulin switch regions but not for intra-switch region recombination or somatic hypermutation. J Exp Med 197 1767 1778
35. SchraderCEBradleySPVardoJMochegovaSNFlanaganE 2003 Mutations occur in the Ig Smu region but rarely in Sgamma regions prior to class switch recombination. Embo J 22 5893 5903
36. StaszewskiOBakerREUcherAJMartierRStavnezerJ 2011 Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig Loci in activated B cells. Mol Cell 41 232 242
37. KobayashiMAidaMNagaokaHBegumNAKitawakiY 2009 AID-induced decrease in topoisomerase 1 induces DNA structural alteration and DNA cleavage for class switch recombination. Proc Natl Acad Sci U S A 106 22375 22380
38. LiuMDukeJLRichterDJVinuesaCGGoodnowCC 2008 Two levels of protection for the B cell genome during somatic hypermutation. Nature 451 841 845
39. WuHYShyySHWangJCLiuLF 1988 Transcription generates positively and negatively supercoiled domains in the template. Cell 53 433 440
40. LiuLFWangJC 1987 Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 84 7024 7027
41. RahmouniARWellsRD 1992 Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J Mol Biol 223 131 144
42. DaynAMalkhosyanSMirkinSM 1992 Transcriptionally driven cruciform formation in vivo. Nucleic Acids Res 20 5991 5997
43. KrasilnikovASPodtelezhnikovAVologodskiiAMirkinSM 1999 Large-scale effects of transcriptional DNA supercoiling in vivo. J Mol Biol 292 1149 1160
44. SamulRLengF 2007 Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains. J Mol Biol 374 925 935
45. NakamuraMKondoSSugaiMNazareaMImamuraS 1996 High frequency class switching of an IgM+ B lymphoma clone CH12F3 to IgA+ cells. Int Immunol 8 193 201
46. RamachandranSChahwanRNepalRMFriederDPanierS 2010 The RNF8/RNF168 ubiquitin ligase cascade facilitates class switch recombination. Proc Natl Acad Sci U S A 107 809 814
47. HanLYuK 2008 Altered kinetics of nonhomologous end joining and class switch recombination in ligase IV-deficient B cells. J Exp Med 205 2745 2753
48. LiXManleyJL 2005 Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122 365 378
49. LarijaniMPetrovAPKolenchenkoOBerruMKrylovSN 2007 AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner. Mol Cell Biol 27 20 30
50. YuKLieberMR 2003 Nucleic acid structures and enzymes in the immunoglobulin class switch recombination mechanism. DNA Repair (Amst) 2 1163 1174
51. ShinkuraRTianMSmithMChuaKFujiwaraY 2003 The influence of transcriptional orientation on endogenous switch region function. Nat Immunol 4 435 441
52. HaddadDOrucZPugetNLaviolette-MaliratNPhilippeM 2011 Sense transcription through the S region is essential for immunoglobulin class switch recombination. Embo J 30 1608 1620
53. YuKRoyDHuangFTLieberMR 2006 Detection and structural analysis of R-loops. Methods Enzymol 409 316 329
54. ZarrinAAAltFWChaudhuriJStokesNKaushalD 2004 An evolutionarily conserved target motif for immunoglobulin class-switch recombination. Nat Immunol 5 1275 1281
55. MasseEDroletM 1999 Escherichia coli DNA topoisomerase I inhibits R-loop formation by relaxing transcription-induced negative supercoiling. J Biol Chem 274 16659 16664
56. CanugoviCSamaranayakeMBhagwatAS 2009 Transcriptional pausing and stalling causes multiple clustered mutations by human activation-induced deaminase. Faseb J 23 34 44
57. RajagopalDMaulRWGhoshAChakrabortyTKhamlichiAA 2009 Immunoglobulin switch mu sequence causes RNA polymerase II accumulation and reduces dA hypermutation. J Exp Med 206 1237 1244
58. WangLWuerffelRFeldmanSKhamlichiAAKenterAL 2009 S region sequence, RNA polymerase II, and histone modifications create chromatin accessibility during class switch recombination. J Exp Med 206 1817 1830
59. DuquetteMLHandaPVincentJATaylorAFMaizelsN 2004 Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev 18 1618 1629
60. LongerichSTanakaABozekGNicolaeDStorbU 2005 The very 5′ end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions. J Exp Med 202 1443 1454
61. MichaelNMartinTENicolaeDKimNPadjenK 2002 Effects of sequence and structure on the hypermutability of immunoglobulin genes. Immunity 16 123 134
62. DunnickWACollinsJTShiJWestfieldGFontaineC 2009 Switch recombination and somatic hypermutation are controlled by the heavy chain 3′ enhancer region. J Exp Med 206 2613 2623
63. MartinAScharffMD 2002 Somatic hypermutation of the AID transgene in B and non-B cells. Proc Natl Acad Sci U S A 99 12304 12308
64. YamaneAReschWKuoNKuchenSLiZ Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes. Nat Immunol 12 62 69
65. ParsaJYBasitWWangCLGommermanJLCarlyleJR 2007 AID mutates a non-immunoglobulin transgene independent of chromosomal position. Mol Immunol 44 567 575
66. ZaheenABoulianneBParsaJYRamachandranSGommermanJL 2009 AID constrains germinal center size by rendering B cells susceptible to apoptosis. Blood 114 547 554
Zvýšte si kvalifikáciu online z pohodlia domova
Nemáte účet? Registrujte sa
Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
