Class-switch recombination (CSR), induced by activation-induced cytidine deaminase (AID), can be divided into two phases: DNA cleavage of the switch (S) regions and the joining of the cleaved ends of the different S regions. Here, we show that the DSIF complex (Spt4 and Spt5), a transcription elongation factor, is required for CSR in a switch-proficient B cell line CH12F3-2A cells, and Spt4 and Spt5 carry out independent functions in CSR. While neither Spt4 nor Spt5 is required for transcription of S regions and AID, expression array analysis suggests that Spt4 and Spt5 regulate a distinct subset of transcripts in CH12F3-2A cells. Curiously, Spt4 is critically important in suppressing cryptic transcription initiating from the intronic Sμ region. Depletion of Spt5 reduced the H3K4me3 level and DNA cleavage at the Sα region, whereas Spt4 knockdown did not perturb the H3K4me3 status and S region cleavage. H3K4me3 modification level thus correlated well with the DNA breakage efficiency. Therefore we conclude that Spt5 plays a role similar to the histone chaperone FACT complex that regulates H3K4me3 modification and DNA cleavage in CSR. Since Spt4 is not involved in the DNA cleavage step, we suspected that Spt4 might be required for DNA repair in CSR. We examined whether Spt4 or Spt5 is essential in non-homologous end joining (NHEJ) and homologous recombination (HR) as CSR utilizes general repair pathways. Both Spt4 and Spt5 are required for NHEJ and HR as determined by assay systems using synthetic repair substrates that are actively transcribed even in the absence of Spt4 and Spt5. Taken together, Spt4 and Spt5 can function independently in multiple transcription-coupled steps of CSR.
Vyšlo v časopise: The DSIF Subunits Spt4 and Spt5 Have Distinct Roles at Various Phases of Immunoglobulin Class Switch Recombination. PLoS Genet 8(4): e32767. doi:10.1371/journal.pgen.1002675 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002675
1. HonjoTKinoshitaKMuramatsuM 2002 Molecular mechanism of class switch recombination: linkage with somatic hypermutation. Annu Rev Immunol 20 165 196
2. CasellasRNussenzweigAWuerffelRPelandaRReichlinA 1998 Ku80 is required for immunoglobulin isotype switching. Embo J 17 2404 2411
3. Pan-HammarstromQJonesAMLahdesmakiAZhouWGattiRA 2005 Impact of DNA ligase IV on nonhomologous end joining pathways during class switch recombination in human cells. J Exp Med 201 189 194
4. YanCTBoboilaCSouzaEKFrancoSHickernellTR 2007 IgH class switching and translocations use a robust non-classical end-joining pathway. Nature 449 478 482
5. LieberMR 2010 The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79 181 211
6. MuramatsuMKinoshitaKFagarasanSYamadaSShinkaiY 2000 Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102 553 563
7. RevyPMutoTLevyYGeissmannFPlebaniA 2000 Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell 102 565 575
8. ArakawaHHauschildJBuersteddeJM 2002 Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion. Science 295 1301 1306
9. HarrisRSSaleJEPetersen-MahrtSKNeubergerMS 2002 AID is essential for immunoglobulin V gene conversion in a cultured B cell line. Curr Biol 12 435 438
10. JungSRajewskyKRadbruchA 1993 Shutdown of class switch recombination by deletion of a switch region control element. Science 259 984 987
11. ZhangJBottaroALiSStewartVAltFW 1993 A selective defect in IgG2b switching as a result of targeted mutation of the I gamma 2b promoter and exon. Embo J 12 3529 3537
12. DoiTKatoLItoSShinkuraRWeiM 2009 The C-terminal region of activation-induced cytidine deaminase is responsible for a recombination function other than DNA cleavage in class switch recombination. Proc Natl Acad Sci U S A 106 2758 2763
13. BarretoVReina-San-MartinBRamiroARMcBrideKMNussenzweigMC 2003 C-terminal deletion of AID uncouples class switch recombination from somatic hypermutation and gene conversion. Mol Cell 12 501 508
14. RanjitSKhairLLinehanEKUcherAJChakrabartiM 2011 AID Binds Cooperatively with UNG and Msh2-Msh6 to Ig Switch Regions Dependent upon the AID C Terminus. J Immunol 187 2464 2475
15. YancopoulosGDDePinhoRAZimmermanKALutzkerSGRosenbergN 1986 Secondary genomic rearrangement events in pre-B cells: VHDJH replacement by a LINE-1 sequence and directed class switching. Embo J 5 3259 3266
16. Stavnezer-NordgrenJSirlinS 1986 Specificity of immunoglobulin heavy chain switch correlates with activity of germline heavy chain genes prior to switching. Embo J 5 95 102
17. NikaidoTNakaiSHonjoT 1981 Switch region of immunoglobulin Cmu gene is composed of simple tandem repetitive sequences. Nature 292 845 848
18. DunnickWHertzGZScappinoLGritzmacherC 1993 DNA sequences at immunoglobulin switch region recombination sites. Nucleic Acids Res 21 365 372
19. HubertLJrLinYDionVWilsonJH 2011 Topoisomerase 1 and Single-Strand Break Repair Modulate Transcription-Induced CAG Repeat Contraction in Human Cells. Mol Cell Biol 31 3105 3112
20. ZhaoJBacollaAWangGVasquezKM 2010 Non-B DNA structure-induced genetic instability and evolution. Cell Mol Life Sci 67 43 62
21. 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
22. BacollaAWojciechowskaMKosmiderBLarsonJEWellsRD 2006 The involvement of non-B DNA structures in gross chromosomal rearrangements. DNA Repair (Amst) 5 1161 1170
23. YuKChedinFHsiehCLWilsonTELieberMR 2003 R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat Immunol 4 442 451
24. RadaCWilliamsGTNilsenHBarnesDELindahlT 2002 Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice. Curr Biol 12 1748 1755
25. ShenHMPoirierMGAllenMJNorthJLalR 2009 The activation-induced cytidine deaminase (AID) efficiently targets DNA in nucleosomes but only during transcription. J Exp Med 206 1057 1071
26. StanlieAAidaMMuramatsuMHonjoTBegumNA 2010 Histone3 lysine4 trimethylation regulated by the facilitates chromatin transcription complex is critical for DNA cleavage in class switch recombination. Proc Natl Acad Sci U S A 107 22190 22195
27. MatthewsAGKuoAJRamon-MaiquesSHanSChampagneKS 2007 RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450 1106 1110
28. BordeVRobineNLinWBonfilsSGeliV 2009 Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites. Embo J 28 99 111
29. SmagulovaFGregorettiIVBrickKKhilPCamerini-OteroRD 2011 Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature 472 375 378
30. WadaTTakagiTYamaguchiYFerdousAImaiT 1998 DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev 12 343 356
31. YamaguchiYInukaiNNaritaTWadaTHandaH 2002 Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol Cell Biol 22 2918 2927
32. ZhangZWuCHGilmourDS 2004 Analysis of polymerase II elongation complexes by native gel electrophoresis. Evidence for a novel carboxyl-terminal domain-mediated termination mechanism. J Biol Chem 279 23223 23228
33. MissraAGilmourDS 2010 Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex. Proc Natl Acad Sci U S A 107 11301 11306
34. AndrulisEDGuzmanEDoringPWernerJLisJT 2000 High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes Dev 14 2635 2649
35. HartzogGAWadaTHandaHWinstonF 1998 Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev 12 357 369
36. ZhouKKuoWHFillinghamJGreenblattJF 2009 Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5. Proc Natl Acad Sci U S A 106 6956 6961
37. FingermanIMDuHNBriggsSD 2008 Controlling histone methylation via trans-histone pathways. Epigenetics 3 237 242
38. WuCHYamaguchiYBenjaminLRHorvat-GordonMWashinskyJ 2003 NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev 17 1402 1414
39. AinbinderEAmir-ZilbersteinLYamaguchiYHandaHDiksteinR 2004 Elongation inhibition by DRB sensitivity-inducing factor is regulated by the A20 promoter via a novel negative element and NF-kappaB. Mol Cell Biol 24 2444 2454
40. PavriRGazumyanAJankovicMDi VirgilioMKleinI 2010 Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5. Cell 143 122 133
41. NakamuraMKondoSSugaiMNazareaMImamuraS 1996 High frequency class switching of an IgM+ B lymphoma clone CH12F3 to IgA+ cells. Int Immunol 8 193 201
42. KomoriTInukaiNYamadaTYamaguchiYHandaH 2009 Role of human transcription elongation factor DSIF in the suppression of senescence and apoptosis. Genes Cells 14 343 354
43. OgiwaraHUiAOtsukaASatohHYokomiI 2011 Histone acetylation by CBP and p300 at double-strand break sites facilitates SWI/SNF chromatin remodeling and the recruitment of non-homologous end joining factors. Oncogene 30 2135 2146
44. SakamotoSIijimaKMochizukiDNakamuraKTeshigawaraK 2007 Homologous recombination repair is regulated by domains at the N - and C-terminus of NBS1 and is dissociated with ATM functions. Oncogene 26 6002 6009
45. PierceAJJohnsonRDThompsonLHJasinM 1999 XRCC3 promotes homology-directed repair of DNA damage in mammalian cells. Genes Dev 13 2633 2638
46. BranzeiDFoianiM 2008 Regulation of DNA repair throughout the cell cycle. Nat Rev Mol Cell Biol 9 297 308
47. BennettCBWestmorelandTJVerrierCSBlanchetteCASabinTL 2008 Yeast screens identify the RNA polymerase II CTD and SPT5 as relevant targets of BRCA1 interaction. PLoS ONE 3 e1448 doi:10.1371/journal.pone.0001448
48. KaplanCDLapradeLWinstonF 2003 Transcription elongation factors repress transcription initiation from cryptic sites. Science 301 1096 1099
49. BradleySPKaminskiDAPetersAHJenuweinTStavnezerJ 2006 The histone methyltransferase Suv39h1 increases class switch recombination specifically to IgA. J Immunol 177 1179 1188
50. SellarsMReina-San-MartinBKastnerPChanS 2009 Ikaros controls isotype selection during immunoglobulin class switch recombination. J Exp Med 206 1073 1087
51. WinstonFChaleffDTValentBFinkGR 1984 Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics 107 179 197
52. MoXDynanWS 2002 Subnuclear localization of Ku protein: functional association with RNA polymerase II elongation sites. Mol Cell Biol 22 8088 8099
53. MaldonadoEShiekhattarRSheldonMChoHDrapkinR 1996 A human RNA polymerase II complex associated with SRB and DNA-repair proteins. Nature 381 86 89
54. HanawaltPCSpivakG 2008 Transcription-coupled DNA repair: two decades of progress and surprises. Nat Rev Mol Cell Biol 9 958 970
55. SchraderCEVardoJLinehanETwarogMZNiedernhoferLJ 2004 Deletion of the nucleotide excision repair gene Ercc1 reduces immunoglobulin class switching and alters mutations near switch recombination junctions. J Exp Med 200 321 330
56. HonjoTNagaokaHShinkuraRMuramatsuM 2005 AID to overcome the limitations of genomic information. Nat Immunol 6 655 661
57. WuerffelRWangLGrigeraFManisJSelsingE 2007 S-S synapsis during class switch recombination is promoted by distantly located transcriptional elements and activation-induced deaminase. Immunity 27 711 722
58. ArakawaHSaribasakHBuersteddeJM 2004 Activation-induced cytidine deaminase initiates immunoglobulin gene conversion and hypermutation by a common intermediate. PLoS Biol 2 e179 doi:10.1371/journal.pone.0000179
59. JiYReschWCorbettEYamaneACasellasR 2010 The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci. Cell 141 419 431
60. MerelliIGuffantiAFabbriMCocitoAFuriaL 2010 RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. Nucleic Acids Res 38 W262 267
61. ZhangMSwansonPC 2008 V(D)J recombinase binding and cleavage of cryptic recombination signal sequences identified from lymphoid malignancies. J Biol Chem 283 6717 6727
62. TsaiAGLuHRaghavanSCMuschenMHsiehCL 2008 Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell 135 1130 1142
63. MarculescuRLeTSimonPJaegerUNadelB 2002 V(D)J-mediated translocations in lymphoid neoplasms: a functional assessment of genomic instability by cryptic sites. J Exp Med 195 85 98
64. YamaneAReschWKuoNKuchenSLiZ 2011 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. GostissaMAltFWChiarleR 2011 Mechanisms that promote and suppress chromosomal translocations in lymphocytes. Annu Rev Immunol 29 319 350
66. Glover-CutterKKimSEspinosaJBentleyDL 2008 RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat Struct Mol Biol 15 71 78
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.
