#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing


Autoři: Tao Chen aff001;  Bin Zhang aff002;  Thomas Ziegenhals aff004;  Archana B. Prusty aff004;  Sebastian Fröhler aff001;  Clemens Grimm aff004;  Yuhui Hu aff002;  Bernhard Schaefke aff002;  Liang Fang aff002;  Min Zhang aff002;  Nadine Kraemer aff006;  Angela M. Kaindl aff006;  Utz Fischer aff004;  Wei Chen aff002
Působiště autorů: Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical System Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany aff001;  Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China aff002;  Cancer Science Institute of Singapore, National University of Singapore, Singapore aff003;  Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany aff004;  Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China aff005;  Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany aff006;  Charité-Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany aff007;  Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children, Berlin, Germany aff008
Vyšlo v časopise: A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing. PLoS Genet 15(10): e32767. doi:10.1371/journal.pgen.1008460
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008460

Souhrn

Malfunction of pre-mRNA processing factors are linked to several human diseases including cancer and neurodegeneration. Here we report the identification of a de novo heterozygous missense mutation in the SNRPE gene (c.65T>C (p.Phe22Ser)) in a patient with non-syndromal primary (congenital) microcephaly and intellectual disability. SNRPE encodes SmE, a basal component of pre-mRNA processing U snRNPs. We show that the microcephaly-linked SmE variant is unable to interact with the SMN complex and as a consequence fails to assemble into U snRNPs. This results in widespread mRNA splicing alterations in fibroblast cells derived from this patient. Similar alterations were observed in HEK293 cells upon SmE depletion that could be rescued by the expression of wild type but not mutant SmE. Importantly, the depletion of SmE in zebrafish causes aberrant mRNA splicing alterations and reduced brain size, reminiscent of the patient microcephaly phenotype. We identify the EMX2 mRNA, which encodes a protein required for proper brain development, as a major mis-spliced down stream target. Together, our study links defects in the SNRPE gene to microcephaly and suggests that alterations of cellular splicing of specific mRNAs such as EMX2 results in the neurological phenotype of the disease.

Klíčová slova:

Fibroblasts – Gene expression – Immunoprecipitation – Introns – Messenger RNA – RNA splicing – Zebrafish – Small nuclear RNA


Zdroje

1. Berget SM, Moore C, Sharp PA. Spliced segments at the 5' terminus of adenovirus 2 late mRNA. PNAS. 1977; 74: 3171–3175. doi: 10.1073/pnas.74.8.3171 269380

2. Chow LT, Gelinas RE, Broker TR, Roberts RJ. An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA. Cell. 1977; 12(1): 1–8. doi: 10.1016/0092-8674(77)90180-5 902310

3. Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA. Are snRNPs involved in splicing? Nature. 1980; 283(5743): 220–224. doi: 10.1038/283220a0 7350545

4. Wahl MC, Will CL, Lührmann R. The Spliceosome: design principles of a dynamic RNP machine. Cell. 2009; 136(4): 701–718. doi: 10.1016/j.cell.2009.02.009 19239890

5. Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, et al. Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength. Genome Biol. 2015; 16(201): 1–21.

6. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008; 40(12): 1413–1415. doi: 10.1038/ng.259 18978789

7. Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010; 463(7280): 457–463. doi: 10.1038/nature08909 20110989

8. Blencowe BJ. Alternative splicing: new insights from global analyses. Cell. 2006; 126(1): 37–47. doi: 10.1016/j.cell.2006.06.023 16839875

9. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008; 456(7221): 470–476. doi: 10.1038/nature07509 18978772

10. Witten JT, Ule J. Understanding splicing regulation through RNA splicing maps. Trends Genet. 2011; 27(3): 89–97. doi: 10.1016/j.tig.2010.12.001 21232811

11. Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, et al. Deciphering the splicing code. Nature. 2010; 465(7294): 53–59. doi: 10.1038/nature09000 20445623

12. Boutz PL, Stoilov P, Li Q, Lin C-H, Chawla G, Ostrow K, et al. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 2007; 21(13): 1636–1652. doi: 10.1101/gad.1558107 17606642

13. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 2011; 471(7339): 473–479. doi: 10.1038/nature09715 21179090

14. Baker BS. Sex in flies: the splice of life. Nature. 1989; 340(6234): 521–524. doi: 10.1038/340521a0 2505080

15. Xie J, Black DL. A CaMK IV responsive RNA element mediates depolarization-induced alternative splicing of ion channels. Nature. 2001; 410(6831): 936–939. doi: 10.1038/35073593 11309619

16. Singh RK, Cooper TA. Pre-mRNA splicing in disease and therapeutics. Trends Mol Med. 2012; 18: 472–482. doi: 10.1016/j.molmed.2012.06.006 22819011

17. Cooper TA, Wan L, Dreyfuss G. RNA and Disease. Cell. 2009; 136(4): 777–793. doi: 10.1016/j.cell.2009.02.011 19239895

18. Niblock M, Gallo J-M. Tau alternative splicing in familial and sporadic tauopathies. Biochemical Soc Trans. 2012; 40(4): 677–680.

19. Comitato A, Spampanato C, Chakarova C, Sanges D, Bhattacharya SS, Marigo V. Mutations in splicing factor PRPF3, causing retinal degeneration, form detrimental aggregates in photoreceptor cells. Hum Mol Genet. 2007; 16(14): 1699–1707. doi: 10.1093/hmg/ddm118 17517693

20. Linder B, Hirmer A, Gal A, Rüther K, Bolz HJ, Winkler C, et al. Identification of a PRPF4 loss-of-function variant that abrogates U4/U6.U5 Tri-snRNP integration and is associated with retinitis pigmentosa. PLoS One. 2014; 9(11): e111754. doi: 10.1371/journal.pone.0111754 25383878

21. Tanackovic G, Ransijn A, Ayuso C, Harper S, Berson Eliot L, Rivolta C. A missense mutation in PRPF6 causes impairment of pre-mRNA splicing and autosomal-dominant retinitis pigmentosa. Am J Hum Genet. 2011; 88(5): 643–649. doi: 10.1016/j.ajhg.2011.04.008 21549338

22. Maubaret CG, Vaclavik V, Mukhopadhyay R, Waseem NH, Churchill A, Holder GE, et al. Autosomal dominant retinitis pigmentosa with intrafamilial variability and incomplete penetrance in two families carrying mutations in PRPF8. Invest Ophthalmol Vis Sci. 2011; 52: 9304–9309. doi: 10.1167/iovs.11-8372 22039234

23. Venturini G, Rose AM, Shah AZ, Bhattacharya SS, Rivolta C. CNOT3 Is a modifier of PRPF31 mutations in retinitis pigmentosa with incomplete penetrance. PLoS Genet. 2012; 8(11): e1003040. doi: 10.1371/journal.pgen.1003040 23144630

24. Linder B, Dill H, Hirmer A, Brocher J, GLee GP, Mathavan S, et al. Systemic splicing factor deficiency causes tissue-specific defects: a zebrafish model for retinitis pigmentosa. Hum Mol Genet. 2011; 20(2): 368–377. doi: 10.1093/hmg/ddq473 21051334

25. Cvačková Z, Matějů D, Staněk D. Retinitis pigmentosa mutations of SNRNP200 enhance cryptic splice-site recognition. Hum Mutat. 2014; 35(3): 308–317. doi: 10.1002/humu.22481 24302620

26. Mordes D, Luo X, Kar A, Kuo D, Xu L, Fushimi K, et al. Pre-mRNA splicing and retinitis pigmentosa. Mol Vis. 2006; 12: 1259–1271. 17110909

27. Lefebvre S, Bürglen L, Reboullet S, Clermont O, Burlet P, Viollet L, et al. Identification and characterization of a spinal muscular atrophy-determining gene. Cell. 1995; 80(1): 155–165. doi: 10.1016/0092-8674(95)90460-3 7813012

28. Zhang Z, Lotti F, Dittmar K, Younis I, Wan L, Kasim M, et al. SMN deficiency causes tissue-specific perturbations in the repertoire of snRNAs and widespread defects in splicing. Cell. 2008; 133(4): 585–600. doi: 10.1016/j.cell.2008.03.031 18485868

29. Lynch DC, Revil T, Schwartzentruber J, Bhoj EJ, Innes AM, Lamont RE, et al. Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro–costo–mandibular syndrome. Nat Commun. 2014; 5: 4483–4488. doi: 10.1038/ncomms5483 25047197

30. Bacrot S, Doyard M, Huber C, Alibeu O, Feldhahn N, Lehalle D, et al. Mutations in SNRPB, encoding components of the core splicing machinery, cause cerebro-costo-mandibular syndrome. Hum Mut. 2015; 36(2): 187–190. doi: 10.1002/humu.22729 25504470

31. Pasternack Sandra M, Refke M, Paknia E, Hennies Hans C, Franz T, Schafer N, et al. Mutations in SNRPE, which encodes a core protein of the spliceosome, cause autosomal-dominant hypotrichosis simplex. Am J Hum Genet. 2013; 92(1): 81–87. doi: 10.1016/j.ajhg.2012.10.022 23246290

32. Edery P, Marcaillou C, Sahbatou M, Labalme A, Chastang J, Touraine R, et al. Association of TALS developmental disorder with defect in minor splicing component U4atac snRNA. Science. 2011; 332(6026): 240–243. doi: 10.1126/science.1202205 21474761

33. He H, Liyanarachchi S, Akagi K, Nagy R, Li J, Dietrich RC, et al. Mutations in U4atac snRNA, a component of the minor spliceosome, in the developmental disorder MOPD I. Science. 2011; 332(6026): 238–240. doi: 10.1126/science.1200587 21474760

34. Neiswanger K, Stanford DR, Sparkes RS, Nishimura D, Mohandas T, Klisak I, et al. Assignment of the gene for the small nuclear ribonucleoprotein E (SNRPE) to human chromosome 1q25–q43. Genomics. 1990; 7(4): 503–508. doi: 10.1016/0888-7543(90)90192-w 2143747

35. Raker VA, Plessel G, Lührmann R. The snRNP core assembly pathway: identification of stable core protein heteromeric complexes and an snRNP subcore particle in vitro. EMBO J. 1996; 15(9): 2256–2269. 8641291

36. Chari A, Golas MM, Klingenhäger M, Neuenkirchen N, Sander B, Englbrecht C, et al. An assembly chaperone collaborates with the SMN complex to generate spliceosomal snRNPs. Cell. 2008; 135(3): 497–509. doi: 10.1016/j.cell.2008.09.020 18984161

37. Grimm C, Chari A, Pelz J-P, Kuper J, Kisker C, Diederichs K, et al. Structural basis of assembly chaperone- mediated snRNP formation. Mol Cell. 2013; 49(4): 692–703. doi: 10.1016/j.molcel.2012.12.009 23333303

38. Meister G, Eggert C, Bühler D, Brahms H, Kambach C, Fischer U. Methylation of Sm proteins by a complex containing PRMT5 and the putative U snRNP assembly factor pICln. Curr Biol. 2001; 11(24): 1990–1994. doi: 10.1016/s0960-9822(01)00592-9 11747828

39. Fischer U, Luhrmann R. (1990) An essential signaling role for the m3G cap in the transport of U1 snRNP to the nucleus. Science. 1990; 249(4970): 786–790. doi: 10.1126/science.2143847 2143847

40. Mouaikel J, Verheggen C, Bertrand E, Tazi J, Bordonné R. Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus. Mol Cell. 2002; 9(4): 891–901. doi: 10.1016/s1097-2765(02)00484-7 11983179

41. Lemm I, Girard C, Kuhn AN, Watkins NJ, Schneider M, Bordonne R, et al. Ongoing U snRNP biogenesis is required for the integrity of cajal bodies. Mol Biol Cell. 2006; 17(7): 3221–3231. doi: 10.1091/mbc.E06-03-0247 16687569

42. Hearst SM, Gilder AS, Negi SS, Davis MD, George EM, Whittom AA, et al. Cajal-body formation correlates with differential coilin phosphorylation in primary and transformed cell lines. J Cell Sci. 2009; 122: 1872–1881. doi: 10.1242/jcs.044040 19435804

43. Prusty AB, Meduri R, Prusty BK, Vanselow J, Schlosser A, Fischer U. Impaired spliceosomal U snRNP assembly leads to Sm mRNA down-regulation and Sm protein degradation. J Cell Biol. 2017; 216(8): 2391–2407. doi: 10.1083/jcb.201611108 28637748

44. So BR, Wan L, Zhang Z, Li P, Babiash E, Duan J, et al. A U1 snRNP–specific assembly pathway reveals the SMN complex as a versatile hub for RNP exchange. Nat Struct Mol Biol. 2016; 23(3): 225–230. doi: 10.1038/nsmb.3167 26828962

45. Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, et al. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 2014; 24(11): 1774–1786. doi: 10.1101/gr.177790.114 25258385

46. Heins N, Cremisi F, Malatesta P, Gangemi RMR, Corte G, Price J, et al. Emx2 promotes symmetric cell divisions and a multipotential fate in precursors from the cerebral cortex. Mol Cell Neurosci. 2001; 18(5): 485–502. doi: 10.1006/mcne.2001.1046 11922140

47. O’Leary DDM, Chou S-J, Sahara S. Area patterning of the mammalian cortex. neuron. 2007; 56(2): 252–269. doi: 10.1016/j.neuron.2007.10.010 17964244

48. Yoshida M, Suda Y, Matsuo I, Miyamoto N, Takeda N, Kuratani S, et al. Emx1 and Emx2 functions in development of dorsal telencephalon. Development. 1997; 124(1): 101–111. 9006071

49. Brunelli S, Faiella A, Capra V, Nigro V, Simeone A, Cama A, et al. Germline mutations in the homeobox gene EMX2 in patients with severe schizencephaly. Nat Genet. 1996; 12(1): 94–96. doi: 10.1038/ng0196-94 8528262

50. Bonnal S, Vigevani L, Valcárcel J. The spliceosome as a target of novel antitumour drugs. Nat Rev Drug Discov. 2012; 11(11): 847–859. doi: 10.1038/nrd3823 23123942

51. Licatalosi DD, Darnell RB. Splicing regulation in neurologic disease. Neuron. 2006; 52(1): 93–101. doi: 10.1016/j.neuron.2006.09.017 17015229

52. Saltzman AL, Pan Q, Blencowe BJ. Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev. 2011; 25(4): 373–384. doi: 10.1101/gad.2004811 21325135

53. Jia Y, Mu John C, Ackerman Susan L. Mutation of a U2 snRNA gene causes global disruption of alternative splicing and neurodegeneration. Cell. 2012; 148(1–2): 296–308. doi: 10.1016/j.cell.2011.11.057 22265417

54. Bezzi M, Teo SX, Muller J, Mok WC, Sahu SK, Vardy LA, et al. Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery. Genes Dev. 2013; 27(17): 1903–1916. doi: 10.1101/gad.219899.113 24013503

55. Bedford MT, Clarke SG. Protein Arginine Methylation in Mammals: Who, What, and Why. Mol Cell. 2009; 33(1): 1–13. doi: 10.1016/j.molcel.2008.12.013 19150423

56. Friesen WJ, Massenet S, Paushkin S, Wyce A, Dreyfuss G. SMN, the product of the spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein targets. Mol Cell. 2001; 7(5): 1111–1117. doi: 10.1016/s1097-2765(01)00244-1 11389857

57. Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol. 2004; 5(10): R74. doi: 10.1186/gb-2004-5-10-r74 15461793

58. Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, et al. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res. 2008; 36(15): 4823–4832. doi: 10.1093/nar/gkn463 18653532

59. Yap K, Lim ZQ, Khandelia P, Friedman B, Makeyev EV. Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Genes Dev. 2012; 26(11): 1209–1223. doi: 10.1101/gad.188037.112 22661231

60. Wong Justin JL, Ritchie W, Ebner Olivia A, Selbach M, Wong Jason WH, Huang Y, et al. Orchestrated intron retention regulates normal granulocyte differentiation. Cell. 2013; 154(3): 583–595. doi: 10.1016/j.cell.2013.06.052 23911323

61. Ge Y, Porse BT. The functional consequences of intron retention: alternative splicing coupled to NMD as a regulator of gene expression. BioEssays. 2014; 36(3): 236–243. doi: 10.1002/bies.201300156 24352796

62. Peng G, Westerfield M. Lhx5 promotes forebrain development and activates transcription of secreted Wnt antagonists. Development. 2006; 133(16): 3191. doi: 10.1242/dev.02485 16854974

63. Peukert D, Weber S, Lumsden A, Scholpp S. Lhx2 and Lhx9 determine neuronal differentiation and compartition in the caudal forebrain by regulating Wnt signaling. PLoS Biol. 2011; 9(12): e1001218. doi: 10.1371/journal.pbio.1001218 22180728

64. Suda Y, Hossain ZM, Kobayashi C, Hatano O, Yoshida M, Matsuo I, et al. Emx2 directs the development of diencephalon in cooperation with Otx2. Development. 2001; 128(13): 2433–2450. 11493561

65. Weiss J, Hurley LA, Harris RM, Finlayson C, Tong M, Fisher LA, et al. ENU mutagenesis in mice identifies candidate genes for hypogonadism. Mamm Genome. 2012; 23(5–6): 346–355. doi: 10.1007/s00335-011-9388-5 22258617

66. Westerfield M. The zebrafish Book: a guide for the laboratory use of zebrafish (Danio Rerio). University of Oregon Press; 1995.

67. Fröhler S, Kieslich M, Langnick C, Feldkamp M, Opgen-Rhein B, Berger F, et al. Exome sequencing helped the fine diagnosis of two siblings afflicted with atypical Timothy syndrome (TS2). BMC Med Genet. 2014; 15: 1–6.

68. Wang Y, Gogol-Döring A, Hu H, Fröhler S, Ma Y, Jens M, et al. Integrative analysis revealed the molecular mechanism underlying RBM10-mediated splicing regulation. EMBO Mol Med. 2013; 5(9): 1431–1442. doi: 10.1002/emmm.201302663 24000153

69. Meister G, Hannus S, Plöttner O, Baars T, Hartmann E, Fakan S, et al. SMNrp is an essential pre-mRNA splicing factor required for the formation of the mature spliceosome. EMBO J. 2001; 20(9): 2304–2314. doi: 10.1093/emboj/20.9.2304 11331595

70. BOCHNIG P, REUTER R, BRINGMANN P, LÜHRMANN R. A monoclonal antibody against 2,2,7-trimethylguanosine that reacts with intact, class U, small nuclear ribonucleoproteins as well as with 7-methylguanosine-capped RNAs. Eur J Biochem. 1987; 168(2): 461–467. doi: 10.1111/j.1432-1033.1987.tb13439.x 2959477

71. Lerner EA, Lerner MR, Janeway CA Jr., Steitz JA. Monoclonal antibodies to nucleic acid-containing cellular constituents: probes for molecular biology and autoimmune disease. PNAS. 1981; 78(5): 2737–2741. doi: 10.1073/pnas.78.5.2737 6789322

Štítky
Genetika Reprodukční medicína

Článek vyšel v časopise

PLOS Genetics


2019 Číslo 10
Nejčtenější tento týden
Nejčtenější v tomto čísle
Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

KOST
Koncepce osteologické péče pro gynekology a praktické lékaře
nový kurz
Autoři: MUDr. František Šenk

Sekvenční léčba schizofrenie
Autoři: MUDr. Jana Hořínková

Hypertenze a hypercholesterolémie – synergický efekt léčby
Autoři: prof. MUDr. Hana Rosolová, DrSc.

Svět praktické medicíny 5/2023 (znalostní test z časopisu)

Imunopatologie? … a co my s tím???
Autoři: doc. MUDr. Helena Lahoda Brodská, Ph.D.

Všechny kurzy
Kurzy Podcasty Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se

#ADS_BOTTOM_SCRIPTS#