TBX3 Regulates Splicing : A Novel Molecular Mechanism for Ulnar-Mammary Syndrome
TBX3 is a protein with essential roles in development and tissue homeostasis, and is implicated in cancer pathogenesis. TBX3 mutations in humans cause a complex of birth defects called Ulnar-mammary syndrome (UMS). Despite the importance of TBX3 and decades of investigation, few TBX3 partner proteins have been identified and little is known about how it functions in cells. Unlike previous investigations focused on TBX3 as DNA binding factor that represses transcription, we took an unbiased approach to identify TBX3 partner proteins in mouse embryos and human cells. We discovered that TBX3 interacts with RNA binding proteins and binds mRNAs to regulate how they are spliced. The different mutations seen in human UMS patients produce mutant proteins that interact with different partners and have different splicing activities. TBX3 promotes or inhibits splicing depending on cellular context, its partner proteins, and the target mRNA. Eukaryotic cells have many more proteins than genes: alternative splicing is critical to generate the different mRNAs needed for production of the specific and vast repertoire of proteins a cell produces. Our finding that TBX3 regulates this process provides fundamental new insights into how altered quantity and molecular function of TBX3 contribute to human developmental disorders and cancer.
Vyšlo v časopise:
TBX3 Regulates Splicing : A Novel Molecular Mechanism for Ulnar-Mammary Syndrome. PLoS Genet 10(3): e32767. doi:10.1371/journal.pgen.1004247
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004247
Souhrn
TBX3 is a protein with essential roles in development and tissue homeostasis, and is implicated in cancer pathogenesis. TBX3 mutations in humans cause a complex of birth defects called Ulnar-mammary syndrome (UMS). Despite the importance of TBX3 and decades of investigation, few TBX3 partner proteins have been identified and little is known about how it functions in cells. Unlike previous investigations focused on TBX3 as DNA binding factor that represses transcription, we took an unbiased approach to identify TBX3 partner proteins in mouse embryos and human cells. We discovered that TBX3 interacts with RNA binding proteins and binds mRNAs to regulate how they are spliced. The different mutations seen in human UMS patients produce mutant proteins that interact with different partners and have different splicing activities. TBX3 promotes or inhibits splicing depending on cellular context, its partner proteins, and the target mRNA. Eukaryotic cells have many more proteins than genes: alternative splicing is critical to generate the different mRNAs needed for production of the specific and vast repertoire of proteins a cell produces. Our finding that TBX3 regulates this process provides fundamental new insights into how altered quantity and molecular function of TBX3 contribute to human developmental disorders and cancer.
Zdroje
1. RodriguezM, AladowiczE, LanfranconeL, GodingCR (2008) Tbx3 represses E-cadherin expression and enhances melanoma invasiveness. Cancer Res 68: 7872–7881.
2. FanW, HuangX, ChenC, GrayJ, HuangT (2004) TBX3 and its isoform TBX3+2a are functionally distinctive in inhibition of senescence and are overexpressed in a subset of breast cancer cell lines. Cancer Res 64: 5132–5139.
3. BrummelkampTR, KortleverRM, LingbeekM, TrettelF, MacDonaldME, et al. (2002) TBX-3, the gene mutated in Ulnar-Mammary Syndrome, is a negative regulator of p19ARF and inhibits senescence. J Biol Chem 277: 6567–6572.
4. ItoA, AsamotoM, HokaiwadoN, TakahashiS, ShiraiT (2005) Tbx3 expression is related to apoptosis and cell proliferation in rat bladder both hyperplastic epithelial cells and carcinoma cells. Cancer Lett 219: 105–112.
5. YaroshW, BarrientosT, EsmailpourT, LinL, CarpenterPM, et al. (2008) TBX3 is overexpressed in breast cancer and represses p14 ARF by interacting with histone deacetylases. Cancer Res 68: 693–699.
6. PlatonovaN, ScottiM, BabichP, BertoliG, MentoE, et al. (2007) TBX3, the gene mutated in ulnar-mammary syndrome, promotes growth of mammary epithelial cells via repression of p19ARF, independently of p53. Cell Tissue Res 328: 301–316.
7. HanJ, YuanP, YangH, ZhangJ, SohBS, et al. (2010) Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature 463: 1096–1100.
8. BakkerML, BoinkGJ, BoukensBJ, VerkerkAO, van den BoogaardM, et al. (2012) T-box transcription factor TBX3 reprogrammes mature cardiac myocytes into pacemaker-like cells. Cardiovasc Res 94: 439–449.
9. FrankDU, CarterKL, ThomasKR, BurrRM, BakkerML, et al. (2012) Lethal arrhythmias in Tbx3-deficient mice reveal extreme dosage sensitivity of cardiac conduction system function and homeostasis. Proc Natl Acad Sci U S A
10. BakkerML, BoukensBJ, MommersteegMT, BronsJF, WakkerV, et al. (2008) Transcription factor Tbx3 is required for the specification of the atrioventricular conduction system. Circ Res 102: 1340–1349.
11. MeneghiniV, OdentS, PlatonovaN, EgeoA, MerloGR (2006) Novel TBX3 mutation data in families with ulnar-mammary syndrome indicate a genotype-phenotype relationship: mutations that do not disrupt the T-domain are associated with less severe limb defects. Eur J Med Genet 49: 151–158.
12. LindenH, WilliamsR, KingJ, BlairE, KiniU (2009) Ulnar Mammary syndrome and TBX3: expanding the phenotype. Am J Med Genet A 149A: 2809–2812.
13. HasdemirC, AydinHH, CelikHA, SimsekE, PayzinS, et al. (2010) Transcriptional profiling of septal wall of the right ventricular outflow tract in patients with idiopathic ventricular arrhythmias. Pacing Clin Electrophysiol 33: 159–167.
14. PfeuferA, van NoordC, MarcianteKD, ArkingDE, LarsonMG, et al. (2010) Genome-wide association study of PR interval. Nat Genet 42: 153–159.
15. CarlsonH, OtaS, CampbellCE, HurlinPJ (2001) A dominant repression domain in Tbx3 mediates transcriptional repression and cell immortalization: relevance to mutations in Tbx3 that cause ulnar-mammary syndrome. Hum Mol Genet 10: 2403–2413.
16. LingbeekME, JacobsJJ, van LohuizenM (2002) The T-box repressors TBX2 and TBX3 specifically regulate the tumor suppressor gene p14ARF via a variant T-site in the initiator. J Biol Chem 277: 26120–26127.
17. CarlsonH, OtaS, SongY, ChenY, HurlinPJ (2002) Tbx3 impinges on the p53 pathway to suppress apoptosis, facilitate cell transformation and block myogenic differentiation. Oncogene 21: 3827–3835.
18. BoogerdKJ, WongLY, ChristoffelsVM, KlarenbeekM, RuijterJM, et al. (2008) Msx1 and Msx2 are functional interacting partners of T-box factors in the regulation of Connexin43. Cardiovasc Res 78: 485–493.
19. BoogerdCJ, WongLY, van den BoogaardM, BakkerML, TessadoriF, et al. (2011) Sox4 mediates Tbx3 transcriptional regulation of the gap junction protein Cx43. Cell Mol Life Sci 68: 3949–3961.
20. DemayF, BilicanB, RodriguezM, CarreiraS, PontecorviM, et al. (2007) T-box factors: targeting to chromatin and interaction with the histone H3 N-terminal tail. Pigment Cell Res 20: 279–287.
21. FrankDU, EmechebeU, ThomasKR, MoonAM (2013) Mouse TBX3 mutants suggest novel molecular mechanisms for Ulnar-mammary syndrome. PLoS One 8: e67841.
22. HoogaarsWM, BarnettP, RodriguezM, CloutDE, MoormanAF, et al. (2008) TBX3 and its splice variant TBX3+exon 2a are functionally similar. Pigment Cell Melanoma Res 21: 379–387.
23. SinghG, CooperTA (2006) Minigene reporter for identification and analysis of cis elements and trans factors affecting pre-mRNA splicing. Biotechniques 41: 177–181.
24. LoganM, MartinJF, NagyA, LobeC, OlsonEN, et al. (2002) Expression of Cre Recombinase in the developing mouse limb bud driven by a Prxl enhancer. Genesis 33: 77–80.
25. FujitaPA, RheadB, ZweigAS, HinrichsAS, KarolchikD, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39: D876–882.
26. CollM, SeidmanJG, MullerCW (2002) Structure of the DNA-bound T-box domain of human TBX3, a transcription factor responsible for ulnar-mammary syndrome. Structure 10: 343–356.
27. PeabodyDS (1993) The RNA binding site of bacteriophage MS2 coat protein. EMBO J 12: 595–600.
28. van den BoogaardM, WongLY, TessadoriF, BakkerML, DreizehnterLK, et al. (2012) Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. J Clin Invest 122: 2519–2530.
29. GardinaPJ, ClarkTA, ShimadaB, StaplesMK, YangQ, et al. (2006) Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 7: 325.
30. LapukA, MarrH, JakkulaL, PedroH, BhattacharyaS, et al. (2010) Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res 8: 961–974.
31. Misquitta-AliCM, ChengE, O'HanlonD, LiuN, McGladeCJ, et al. (2011) Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol Cell Biol 31: 138–150.
32. BrugioloM, HerzelL, NeugebauerKM (2013) Counting on co-transcriptional splicing. F1000Prime Rep 5: 9.
33. KuliszA, SimonHG (2008) An evolutionarily conserved nuclear export signal facilitates cytoplasmic localization of the Tbx5 transcription factor. Mol Cell Biol 28: 1553–1564.
34. PonicsanSL, KugelJF, GoodrichJA (2010) Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev 20: 149–155.
35. LucoRF, AlloM, SchorIE, KornblihttAR, MisteliT (2011) Epigenetics in alternative pre-mRNA splicing. Cell 144: 16–26.
36. HnilicovaJ, HozeifiS, DuskovaE, IchaJ, TomankovaT, et al. (2011) Histone deacetylase activity modulates alternative splicing. PLoS One 6: e16727.
37. DavidCJ, ChenM, AssanahM, CanollP, ManleyJL (2010) HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer. Nature 463: 364–368.
38. Golan-GerstlR, CohenM, ShiloA, SuhSS, BakacsA, et al. (2011) Splicing factor hnRNP A2/B1 regulates tumor suppressor gene splicing and is an oncogenic driver in glioblastoma. Cancer Res 71: 4464–4472.
39. XiaoR, TangP, YangB, HuangJ, ZhouY, et al. (2012) Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. Mol Cell 45: 656–668.
40. HuelgaSC, VuAQ, ArnoldJD, LiangTY, LiuPP, et al. (2012) Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep 1: 167–178.
41. AuboeufD, DowhanDH, KangYK, LarkinK, LeeJW, et al. (2004) Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes. Proc Natl Acad Sci U S A 101: 2270–2274.
42. MontanoMM, EkenaK, Delage-MourrouxR, ChangW, MartiniP, et al. (1999) An estrogen receptor-selective coregulator that potentiates the effectiveness of antiestrogens and represses the activity of estrogens. Proc Natl Acad Sci U S A 96: 6947–6952.
43. WillemsP, De RuyckK, Van den BroeckeR, MakarA, PerlettiG, et al. (2009) A polymorphism in the promoter region of Ku70/XRCC6, associated with breast cancer risk and oestrogen exposure. J Cancer Res Clin Oncol 135: 1159–1168.
44. van DijkTB, GillemansN, SteinC, FanisP, DemmersJ, et al. (2010) Friend of Prmt1, a novel chromatin target of protein arginine methyltransferases. Mol Cell Biol 30: 260–272.
45. BertuccioP, ChatenoudL, LeviF, PraudD, FerlayJ, et al. (2009) Recent patterns in gastric cancer: a global overview. Int J Cancer 125: 666–673.
46. LeeCG (2002) RH70, a bidirectional RNA helicase, co-purifies with U1snRNP. J Biol Chem 277: 39679–39683.
47. LiuZR (2002) p68 RNA helicase is an essential human splicing factor that acts at the U1 snRNA-5′ splice site duplex. Mol Cell Biol 22: 5443–5450.
48. HonigA, AuboeufD, ParkerMM, O'MalleyBW, BergetSM (2002) Regulation of alternative splicing by the ATP-dependent DEAD-box RNA helicase p72. Mol Cell Biol 22: 5698–5707.
49. GuilS, GattoniR, CarrascalM, AbianJ, SteveninJ, et al. (2003) Roles of hnRNP A1, SR proteins, and p68 helicase in c-H-ras alternative splicing regulation. Mol Cell Biol 23: 2927–2941.
50. GovoniKE, LinaresGR, ChenST, PourteymoorS, MohanS (2009) T-box 3 negatively regulates osteoblast differentiation by inhibiting expression of osterix and runx2. J Cell Biochem 106: 482–490.
51. KurtevV, MargueronR, KrobothK, OgrisE, CavaillesV, et al. (2004) Transcriptional regulation by the repressor of estrogen receptor activity via recruitment of histone deacetylases. J Biol Chem 279: 24834–24843.
52. WillisDM, LoewyAP, Charlton-KachigianN, ShaoJS, OrnitzDM, et al. (2002) Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex. J Biol Chem 277: 37280–37291.
53. DowhanDH, HongEP, AuboeufD, DennisAP, WilsonMM, et al. (2005) Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta. Mol Cell 17: 429–439.
54. FanC, ChenQ, WangQK (2009) Functional role of transcriptional factor TBX5 in pre-mRNA splicing and Holt-Oram syndrome via association with SC35. J Biol Chem 284: 25653–25663.
55. NaylerO, StratlingW, BourquinJP, StagljarI, LindemannL, et al. (1998) SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements. Nucleic Acids Res 26: 3542–3549.
56. DaviesRC, CalvioC, BrattE, LarssonSH, LamondAI, et al. (1998) WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes Dev 12: 3217–3225.
57. MarkusMA, HeinrichB, RaitskinO, AdamsDJ, MangsH, et al. (2006) WT1 interacts with the splicing protein RBM4 and regulates its ability to modulate alternative splicing in vivo. Exp Cell Res 312: 3379–3388.
58. CassidayLA, MaherLJ3rd (2002) Having it both ways: transcription factors that bind DNA and RNA. Nucleic Acids Res 30: 4118–4126.
59. DavisBN, HilyardAC, NguyenPH, LagnaG, HataA (2010) Smad proteins bind a conserved RNA sequence to promote microRNA maturation by Drosha. Mol Cell 39: 373–384.
60. Abdul-MananN, WilliamsKR (1996) hnRNP A1 binds promiscuously to oligoribonucleotides: utilization of random and homo-oligonucleotides to discriminate sequence from base-specific binding. Nucleic Acids Res 24: 4063–4070.
61. TomonagaT, LevensD (1995) Heterogeneous nuclear ribonucleoprotein K is a DNA-binding transactivator. J Biol Chem 270: 4875–4881.
62. CaricasoleA, DuarteA, LarssonSH, HastieND, LittleM, et al. (1996) RNA binding by the Wilms tumor suppressor zinc finger proteins. Proc Natl Acad Sci U S A 93: 7562–7566.
63. SuswamEA, LiYY, MahtaniH, KingPH (2005) Novel DNA-binding properties of the RNA-binding protein TIAR. Nucleic Acids Res 33: 4507–4518.
64. BamshadM, LeT, WatkinsWS, DixonME, KramerBE, et al. (1999) The spectrum of mutations in TBX3: genotype/pheotype relationship in Ulnar-Mammary Syndrome. Am J Hum Genet 64: 1550–1562.
65. FranklinS, ZhangMJ, ChenH, PaulssonAK, Mitchell-JordanSA, et al. (2011) Specialized compartments of cardiac nuclei exhibit distinct proteomic anatomy. Mol Cell Proteomics 10 M110 000703.
66. FranklinS, ChenH, Mitchell-JordanS, RenS, WangY, et al. (2012) Quantitative analysis of the chromatin proteome in disease reveals remodeling principles and identifies high mobility group protein b2 as a regulator of hypertrophic growth. Mol Cell Proteomics 11 M111 014258.
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