Alternative splicing of mRNA in the molecular pathology of neurodegenerative diseases

Neurobiology of Aging

Volumn 33, Issue 5, 2012, Pages 1012.e11-1012.e24

  Mills, James Dominic ^a   Janitz, Michal ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Alternative splicing; Alzheimer's disease; Neurodegenerative diseases; Parkinson's disease; RNA Seq; Transcriptome

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; ALZHEIMER DISEASE; APOE GENE; APP GENE; BACE GENE; BDNF GENE; CORTICOBASAL DEGENERATION; DEGENERATIVE DISEASE; DNA MICROARRAY; EXON; FRONTOTEMPORAL DEMENTIA; GENE; GENETIC ANALYSIS; GRN GENE; HUMAN; HUNTINGTON CHOREA; MAPT GENE; NONHUMAN; PARK2 GENE; PARKINSON DISEASE; PICK PRESENILE DEMENTIA; PIN1 GENE; PRIORITY JOURNAL; PROGRESSIVE SUPRANUCLEAR PALSY; PSEN1 GENE; PSEN2 GENE; RBFOX1 GENE; RBFOX2 GENE; RBFOX3 GENE; REVIEW; RNA SEQUENCE; SNCA GENE; SPINOCEREBELLAR DEGENERATION; SRRM2 GENE;

EID: 84858334551     PISSN: 01974580     EISSN: 15581497     Source Type: Journal    
DOI: 10.1016/j.neurobiolaging.2011.10.030     Document Type: Review

References (143)

1. Altar C.A., Vawter M.P., Ginsberg S.D. Target identification for CNS diseases by transcriptional profiling. Neuropsychopharmacology 2009, 34:18-54.
2. Atz M., Walsh D., Cartagena P., Li J., Evans S., Choudary P., Overman K., Stein R., Tomita H., Potkin S., Myers R., Watson S.J., Jones E.G., Akil H., Bunney W.E., Vawter M.P. Methodological considerations for gene expression profiling of human brain. J. Neurosci. Methods 2007, 163:295-309.
3. Auweter S.D., Fasan R., Reymond L., Underwood J.G., Black D.L., Pitsch S., Allain F.H. Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO 2006, 25:163-173.
4. Baker M., Mackenzie I.R., Pickering-Brown S.M., Gass J., Rademakers R., Lindholm C., Snowden J., Adamson J., Sadovnick A.D., Rollinson S., Cannon A., Dwosh E., Neary D., Melquist S., Richardson A., Dickson D., Berger Z., Eriksen J., Robinson T., Zehr C., Dickey C.A., Crook R., McGowan E., Mann D., Boeve B., Feldman H., Hutton M. Mutations in progranulin cause tau-negative frontotemporal dementia linked to chromosome 17. Nature 2006, 442:916-919.
5. Bardien S., Keyser R., Yako Y., Lombard D., Carr J. Molecular analysis of the parkin gene in South African patients diagnosed with Parkinson's disease. Parkinsonism Relat. Disord. 2009, 15:116-121.
6. Barnby G., Abbott A., Sykes N., Morris A., Weeks D.E., Mott R., Lamb J., Bailey A.J., Monaco A.P. Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT. Am. J. Hum. Genet. 2005, 76:950-966.
7. Barsottini O.G., Felicio A.C., Aguiar Pde C., Godeiro-Junior C., Shih M.C., Hoexter M.Q., Bressan R.A., Ferraz H.B., Andrade L.A. Clinical and molecular neuroimaging characteristics of Brazilian patients with Parkinson's disease and mutations in PARK2 or PARK8 genes. Arq. Neuropsiquiatr. 2009, 67:7-11.
8. Baulac S., LaVoie M.J., Kimberly W.T., Strahle J., Wolfe M.S., Selkoe D.J., Xia W. Functional gamma-secretase complex assembly in Golgi/trans-Golgi network: interactions among presenilin, nicastrin, Aph1, Pen-2, and gamma-secretase substrates. Neurobiol. Dis. 2003, 14:194-204. 10.1016/S0969-9961(03)00123-2.
9. Bekris L.M., Mata I.F., Zabetian C.P. The genetics of Parkinson disease. J. Geriatr. Psychiatry Neurol. 2010, 23:228-242.
10. Bertoli-Avella A.M., Giroud-Benitez J.L., Akyol A., Barbosa E., Schaap O., van der Linde H.C., Martignoni E., Lopiano L., Lamberti P., Fincati E., Antonini A., Stocchi F., Montagna P., Squitieri F., Marini P., Abbruzzese G., Fabbrini G., Marconi R., Dalla Libera A., Trianni G., Guidi M., De Gaetano A., Boff Maegawa G., De Leo A., Gallai V., de Rosa G., Vanacore N., Meco G., van Duijn C.M., Oostra B.A., Heutink P., Bonifati V. Novel parkin mutations detected in patients with early-onset Parkinson's disease. Mov. Disord. 2005, 20:424-431.
11. Beyer K. Alpha-synuclein structure, posttranslational modification, and alternative splicing as aggregation enhancers. Acta Neuropathol. 2006, 112:237-251.
12. Beyer K., Lao J.I., Carrato C., Mate J.L., Lopez D., Ferrer I., Ariza A. Differential expression of alpha-synuclein isoforms in dementia with Lewy bodies. Neuropathol. Appl. Neurobiol. 2004, 20:601-607.
13. Bhalla K., Phillips H.A., Crawford J., McKenzie O.L., Mulley J.C., Eyre H., Gardner A.E., Kremmidiotis G., Callen D.F. The de novo chromosome 16 translocations of two patients with abnormal phenotypes (mental retardation and epilepsy) disrupt the A2BP1 gene. J. Hum. Genet. 2004, 49:308-311.
14. Blencowe B.J. Alternative splicing: new insights from global analyses. Cell 2006, 126:37-47.
15. Braak H., Braak E. Neuropathological staging of Alzheimer-related changes. Acta Neuropathol. 1991, 82:239-259.
16. Brouwers N., Nuytemans K., van der Zee J., Gijselinck I., Engelborghs S., Theuns J., Kumar-Singh S., Pickut B.A., Pals P., Dermaut B., Bogaerts V., De Pooter T., Serneels S., Van den Broeck M., Cuijt I., Mattheijssens M., Peeters K., Sciot R., Martin J.J., Cras P., Santens P., Vandenberghe R., De Deyn P.P., Cruts M., Van Broeckhoven C., Sleegers K. Alzheimer and Parkinson diagnoses in progranulin null mutation carriers in an extended founder family. Arch. Neurol. 2007, 64:1436-1446.
17. Campion D., Martin C., Heilig R., Charbonnier F., Moreau V., Flaman J.M., Petit J.L., Hannequin D., Brice A., Frebourg T. The NACP/synuclein gene: chromosomal assignment and screening for alterations in Alzheimer disease. Genomics 1995, 26:254-257. 10.1016/0888-7543(95)80208-4.
18. Cartegni L., Chew S.L., Krainer A.R. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet. 2002, 3:285-298.
19. Carter H.B., Morrell C.H., Pearson J.D., Brant L.J., Plato C.C., Metter E.J., Chan D.W., Fozard J.L., Walsh P.C. Estimation of prostatic growth using serial prostate-specific antigen measurements in men with and without prostate disease. Cancer Res. 1992, 52:3323-3328.
20. Carter H.B., Pearson J.D., Metter E.J., Brant L.J., Chan D.W., Andres R., Fozard J.L., Walsh P.C. Longitudinal evaluation of prostate-specific antigen levels in men with and without prostate disease. JAMA 1992, 267:2215-2220.
21. Cattaneo E., Rigamonti D., Goffredo D., Zuccato C., Squitieri F., Sipione S. Loss of normal huntingtin function: new developments in Huntington's disease research. Trends Neurosci. 2001, 24:182-188. 10.1016/S0166-2236(00)01721-5.
22. Corder E.H., Saunders A.M., Risch N.J., Strittmatter W.J., Schmechel D.E., Gaskell P.C., Rimmler J.B., Locke P.A., Conneally P.M., Schmader K.E., et al. Protective effect of apolipoprotein E type 2 allele for late onset Alzheimer disease. Nat. Genet. 1994, 7:180-184.
23. Cortini F., Fenoglio C., Guidi I., Venturelli E., Pomati S., Marcone A., Scalabrini D., Villa C., Clerici F., Dalla Valle E., Mariani C., Cappa S., Bresolin N., Scarpini E., Galimberti D. Novel exon 1 progranulin gene variant in Alzheimer's disease. Eur. J. Neurol. 2008, 15:1111-1117.
24. Courtney E., Kornfeld S., Janitz K., Janitz M. Transcriptome profiling in neurodegenerative disease. J. Neurosci. Methods 2010, 193:189-202.
25. Cowburn R.F., Vestling M., Fowler C.J., Ravid R., Winblad B., O'Neill C. Disrupted beta 1-adrenoceptor-G protein coupling in the temporal cortex of patients with Alzheimer's disease. Neurosci. Lett. 1993, 155:163-166. 10.1016/0304-3940(93)90698-K.
26. Cross A.J., Crow T.J., Ferrier I.N., Johnson J.A. The selectivity of the reduction of serotonin S2 receptors in Alzheimer-type dementia. Neurobiol. Aging 1986, 7:3-7. 10.1016/0197-4580(86)90019-9.
27. Cruts M., Gijselinck I., van der Zee J., Engelborghs S., Wils H., Pirici D., Rademakers R., Vandenberghe R., Dermaut B., Martin J.J., van Duijn C., Peeters K., Sciot R., Santens P., De Pooter T., Mattheijssens M., Van den Broeck M., Cuijt I., Vennekens K., De Deyn P.P., Kumar-Singh S., Van Broeckhoven C. Null mutations in progranulin cause ubiquitin-positive frontotemporal dementia linked to chromosome 17q21. Nature 2006, 442:920-924.
28. Cruts M., Van Broeckhoven C. Presenilin mutations in Alzheimer's disease. Hum. Mutat. 1998, 11:183-190. 10.1002/(SICI)1098-1004(1998)11:3.
29. De Jonghe C., Cruts M., Rogaeva E.A., Tysoe C., Singleton A., Vanderstichele H., Meschino W., Dermaut B., Vanderhoeven I., Backhovens H., Vanmechelen E., Morris C.M., Hardy J., Rubinsztein D.C., St George-Hyslop P.H., Van Broeckhoven C. Aberrant splicing in the presenilin-1 intron 4 mutation causes presenile Alzheimer's disease by increased Abeta42 secretion. Hum. Mol. Genet. 1999, 8:1529-1540.
30. De Strooper B., Saftig P., Craessaerts K., Vanderstichele H., Guhde G., Annaert W., Von Figura K., Van Leuven F. Deficiency of presenilin-1 inhibits the normal cleavage of amyloid precursor protein. Nature 1998, 391:387-390.
31. Donev R., Newall A., Thome J., Sheer D. A role for SC35 and hnRNPA1 in the determination of amyloid precursor protein isoforms. Mol. Psychiatry 2007, 12:681-690.
32. Elliott D.J. Splicing and the single cell. Histol. Histopathol. 2000, 15:239-249.
33. Faustino N.A., Cooper T.A. Pre-mRNA splicing and human disease. Genes Dev. 2003, 17:419-437.
34. Fratiglioni L., De Ronchi D., Agüero-Torres H. Worldwide prevalence and incidence of dementia. Drugs Aging 1999, 15:365-375.
35. Fusco F.R., Chen Q., Lamoreaux W.J., Figueredo-Cardenas G., Jiao Y., Coffman J.A., Surmeier D.J., Honig M.G., Carlock L.R., Reiner A. Cellular localization of huntingtin in striatal and cortical neurons in rats: lack of correlation with neuronal vulnerability in Huntington's disease. J. Neurosci. 1999, 19:1189-1202.
36. Fusco F.R., Zuccato C., Tartari M., Martorana A., De March Z., Giampà C., Cattaneo E., Bernardi G. Co-localization of brain-derived neurotrophic factor (BDNF) and wild-type huntingtin in normal and quinolinic acid-lesioned rat brain. Eur. J. Neurosci. 2003, 18:1093-1102.
37. Gardina P.J., Clark T.A., Shimada B., Staples M.K., Yang Q., Veitch J., Schweitzer A., Awad T., Sugnet C., Dee S., Davies C., Williams A., Turpaz Y. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 2006, 7:325.
38. Gehman L.T., Stoilov P., Maguire J., Damianov A., Lin C.H., Shiue L., Ares M., Mody I., Black D.L. The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat. Genet. 2011, 43:706-711.
39. Geisler S., Holmström K.M., Skujat D., Fiesel F.C., Rothfuss O.C., Kahle P.J., Springer W. PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat. Cell Biol. 2010, 12:119-131.
40. George J.M. The synucleins. Genome Biol. 2002, 3. REVIEWS3002.
41. Geula C., Mesulam M.M. Cholinesterases and the pathology of Alzheimer disease. Alzheimer Dis. Assoc. Disord. 1995, 9(suppl 2):23-28.
42. Gijselinck I., Van Broeckhoven C., Cruts M. Granulin mutations associated with frontotemporal lobar degeneration and related disorders: an update. Hum. Mutat. 2008, 29:1373-1386.
43. Goedert M., Jakes R., Crowther R.A. Effects of frontotemporal dementia FTDP-17 mutations on heparin-induced assembly of tau filaments. FEBS Lett. 1999, 450:306-311. 10.1016/S0014-5793(99)00508-6.
44. Goedert M., Spillantini M.G., Jakes R., Rutherford D., Crowther R.A. Multiple isoforms of human microtubule-associated protein tau: sequences and localization in neurofibrillary tangles of Alzheimer's disease. Neuron 1989, 3:519-526. 10.1016/0896-6273(89)90210-9.
45. Goffredo D., Rigamonti D., Zuccato C., Tartari M., Valenza M., Cattaneo E. Prevention of cytosolic IAPs degradation: a potential pharmacological target in Huntington's disease. Pharmacol. Res. 2005, 52:140-150.
46. Golde T.E., Estus S., Usiak M., Younkin L.H., Younkin S.G. Expression of beta amyloid protein precursor mRNAs: recognition of a novel alternatively spliced form and quantitation in Alzheimer's disease using PCR. Neuron 1990, 4:253-267. 10.1016/0896-6273(90)90100-T.
47. Graff-Radford N.R., Woodruff B.K. Frontotemporal dementia. Semin. Neurol. 2007, 27:48-57.
48. Gregory T.R. A bird's-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves. Evolution 2002, 56:121-130.
49. Hallegger M., Llorian M., Smith C.W. Alternative splicing: global insights. FEBS J. 2010, 277:856-866.
50. Hudson T.J., Anderson W., Artez A., Barker A.D., Bell C., Bernabe R.R., Bhan M.K., Calvo F., Eerola I., Gerhard D.S., Guttmacher A., Guyer M., Hemsley F.M., Jennings J.L., Kerr D., Klatt P., Kolar P., Kusada J., Lane D.P., Laplace F., Youyong L., Nettekoven G., Ozenberger B., Peterson J., Rao T.S., Remacle J., Schafer A.J., Shibata T., Stratton M.R., Vockley J.G., Watanabe K., Yang H., Yuen M.M., Knoppers B.M., Bobrow M., Cambon-Thomsen A., Dressler L.G., Dyke S.O., Joly Y., Kato K., Kennedy K.L., Nicolas P., Parker M.J., Rial-Sebbag E., Romeo-Casabona C.M., Shaw K.M., Wallace S., Wiesner G.L., Zeps N., Lichter P., Biankin A.V., Chabannon C., Chin L., Clement B., de Alava E., Degos F., Ferguson M.L., Geary P., Hayes D.N., Johns A.L., Kasprzyk A., Nakagawa H., Penny R., Piris M.A., Sarin R., Scarpa A., van de Vijver M., Futreal P.A., Aburatani H., Bayes M., Botwell D.D., Campbell P.J., Estivill X., Grimmond S.M., Gut I., Hirst M., Lopez-Otin C., Majumder P., Marra M., McPherson J.D., Ning Z., Puente X.S., Ruan Y., Stunnenberg H.G., Swerdlow H., Velculescu V.E., Wilson R.K., Xue H.H., Yang L., Spellman P.T., Bader G.D., Boutros P.C., Flicek P., Getz G., Guigo R., Guo G., Haussler D., Heath S., Hubbard T.J., Jiang T., Jones S.M., Li Q., Lopez-Bigas N., Luo R., Muthuswamy L., Ouellette B.F., Pearson J.V., Quesada V., Raphael B.J., Sander C., Speed T.P., Stein L.D., Stuart J.M., Teague J.W., Totoki Y., Tsunoda T., Valencia A., Wheeler D.A., Wu H., Zhao S., Zhou G., Lathrop M., Thomas G., Yoshida T., Axton M., Gunter C., Miller L.J., Zhang J., Haider S.A., Wang J., Yung C.K., Cross A., Liang Y., Gnaneshan S., Guberman J., Hsu J., Chalmers D.R., Hasel K.W., Kaan T.S., Lowrance W.W., Masui T., Rodriguez L.L., Vergely C., Bowtell D.D., Cloonan N., deFazio A., Eshleman J.R., Etemadmoghadam D., Gardiner B.A., Kench J.G., Sutherland R.L., Tempero M.A., Waddell N.J., Wilson P.J., Gallinger S., Tsao M.S., Shaw P.A., Petersen G.M., Mukhopadhyay D., DePinho R.A., Thayer S., Shazand K., Beck T., Sam M., Timms L., Ballin V., Lu Y., Ji J., Zhang X., Chen F., Hu X., Yang Q., Tian G., Zhang L., Xing X., Li X., Zhu Z., Yu Y., Yu J., Tost J., Brennan P., Holcatova I., Zaridze D., Brazma A., Egevard L., Prokhortchouk E., Banks R.E., Uhlen M., Viksna J., Ponten F., Skryabin K., Birney E., Borg A., Borresen-Dale A.L., Caldas C., Foekens J.A., Martin S., Reis-Filho J.S., Richardson A.L., Sotiriou C., Thoms G., van't Veer L., Birnbaum D., Blanche H., Boucher P., Boyault S., Masson-Jacquemier J.D., Pauporte I., Pivot X., Vincent-Salomon A., Tabone E., Theillet C., Treilleux I., Bioulac-Sage P., Decaens T., Franco D., Gut M., Samuel D., Zucman-Rossi J., Eils R., Brors B., Korbel J.O., Korshunov A., Landgraf P., Lehrach H., Pfister S., Radlwimmer B., Reifenberger G., Taylor M.D., von Kalle C., Majumder P.P., Pederzoli P., Lawlor R.A., Delledonne M., Bardelli A., Gress T., Klimstra D., Zamboni G., Nakamura Y., Miyano S., Fujimoto A., Campo E., de Sanjose S., Montserrat E., Gonzalez-Diaz M., Jares P., Himmelbaue H., Bea S., Aparicio S., Easton D.F., Collins F.S., Compton C.C., Lander E.S., Burke W., Green A.R., Hamilton S.R., Kallioniemi O.P., Ley T.J., Liu E.T., Wainwright B.J. International network of cancer genome projects. Nature 2010, 464:993-998.
51. Illarioshkin S.N., Periquet M., Rawal N., Lücking C.B., Zagorovskaya T.B., Slominsky P.A., Miloserdova O.V., Markova E.D., Limborska S.A., Ivanova-Smolenskaya I.A., Brice A. Mutation analysis of the parkin gene in Russian families with autosomal recessive juvenile parkinsonism. Mov. Disord. 2003, 18:914-919.
52. A haplotype map of the human genome. Nature 2005, 437:1299-1320. International HapMap Consortium.
53. Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945. International Human Genome Sequencing Consortium.
54. Jacobsen J.S., Blume A.J., Vitek M.P. Quantitative measurement of alternatively spliced amyloid precursor protein mRNA expression in Alzheimer's disease and normal brain by S1 nuclease protection analysis. Neurobiol. Aging 1991, 12:585-592. 10.1016/0197-4580(91)90090-7.
55. Janitz M. Next-Generation Genome Sequencing-Towards Personalised Medicine 2008, Wiley-VCH, Weinheim, Germany.
56. Jin Y., Suzuki H., Maegawa S., Endo H., Sugano S., Hashimoto K., Yasuda K., Inoue K. A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO 2003, 22:905-912.
57. Johnson M.B., Kawasawa Y.I., Mason C.E., Krsnik Z., Coppola G., Bogdanović D., Geschwind D.H., Mane S.M., State M.W., Sestan N. Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 2009, 62:494-509.
58. Jorm A.F., Dear K.B., Burgess N.M. Projections of future numbers of dementia cases in Australia with and without prevention. Aust. N. Z. J. Psychiatry 2005, 39:959-963.
59. Kang J., Lemaire H.G., Unterbeck A., Salbaum J.M., Masters C.L., Grzeschik K.H., Multhaup G., Beyreuther K., Müller-Hill B. The precursor of Alzheimer's disease amyloid A4 protein resembles a cell-surface receptor. Nature 1987, 325:733-736.
60. Kann M., Jacobs H., Mohrmann K., Schumacher K., Hedrich K., Garrels J., Wiegers K., Schwinger E., Pramstaller P.P., Breakefield X.O., Ozelius L.J., Vieregge P., Klein C. Role of parkin mutations in 111 community-based patients with early-onset parkinsonism. Ann. Neurol. 2002, 51:621-625.
61. Kapur K., Xing Y., Ouyang Z., Wong W.H. Exon arrays provide accurate assessments of gene expression. Genome Biol. 2007, 8:R82.
62. Kitada T., Asakawa S., Hattori N., Matsumine H., Yamamura Y., Minoshima S., Yokochi M., Mizuno Y., Shimizu N. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 1998, 392:605-608.
63. Kitaguchi N., Takahashi Y., Tokushima Y., Shiojiri S., Ito H. Novel precursor of Alzheimer's disease amyloid protein shows protease inhibitory activity. Nature 1988, 331:530-532.
64. Kok E., Haikonen S., Luoto T., Huhtala H., Goebeler S., Haapasalo H., Karhunen P.J. Apolipoprotein E-dependent accumulation of Alzheimer disease-related lesions begins in middle age. Ann. Neurol. 2009, 65:650-657.
65. König G., Mönning U., Czech C., Prior R., Banati R., Schreiter-Gasser U., Bauer J., Masters C.L., Beyreuther K. Identification and differential expression of a novel alternative splice isoform of the beta A4 amyloid precursor protein (APP) mRNA in leukocytes and brain microglial cells. J. Biol. Chem. 1992, 267:10804-10809.
66. Le Ber I., van der Zee J., Hannequin D., Gijselinck I., Campion D., Puel M., Laquerrière A., De Pooter T., Camuzat A., Van den Broeck M., Dubois B., Sellal F., Lacomblez L., Vercelletto M., Thomas-Antérion C., Michel B.F., Golfier V., Didic M., Salachas F., Duyckaerts C., Cruts M., Verpillat P., Van Broeckhoven C., Brice A. Progranulin null mutations in both sporadic and familial frontotemporal dementia. Hum. Mutat. 2007, 28:846-855.
67. Lee J.A., Tang Z.Z., Black D.L. An inducible change in Fox-1/A2BP1 splicing modulates the alternative splicing of downstream neuronal target exons. Genes Dev. 2009, 23:2284-2293.
68. Lee V.M., Goedert M., Trojanowski J.Q. Neurodegenerative tauopathies. Annu. Rev. Neurosci. 2001, 24:1121-1159.
69. Lesage S., Brice A. Parkinson's disease: from monogenic forms to genetic susceptibility factors. Hum. Mol. Genet. 2009, 18:R48-R59.
70. Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18:1851-1858.
71. Li R., Li Y., Kristiansen K., Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714.
72. Lim J., Crespo-Barreto J., Jafar-Nejad P., Bowman A.B., Richman R., Hill D.E., Orr H.T., Zoghbi H.Y. Opposing effects of polyglutamine expansion on native protein complexes contribute to SCA1. Nature 2008, 452:713-718.
73. Liou Y.C., Sun A., Ryo A., Zhou X.Z., Yu Z.X., Huang H.K., Uchida T., Bronson R., Bing G., Li X., Hunter T., Lu K.P. Role of the prolyl isomerase Pin1 in protecting against age-dependent neurodegeneration. Nature 2003, 424:556-561.
74. Lobo A., Launer L.J., Fratiglioni L., Andersen K., Di Carlo A., Breteler M.M., Copeland J.R., Dartigues J.F., Jagger C., Martinez-Lage J., Soininen H., Hofman A. Prevalence of dementia and major subtypes in Europe: a collaborative study of population-based cohorts. Neurologic Diseases in the Elderly Research Group. Neurology 2000, 54(suppl 5):S4-S9.
75. Lücking C.B., Dürr A., Bonifati V., Vaughan J., De Michele G., Gasser T., Harhangi B.S., Meco G., Denèfle P., Wood N.W., Agid Y., Brice A. Association between early-onset Parkinson's disease and mutations in the parkin gene. N. Engl. J. Med. 2000, 342:1560-1567.
76. Mandel S., Grunblatt E., Riederer P., Amariglio N., Jacob-Hirsch J., Rechavi G., Youdim M.B. Gene expression profiling of sporadic Parkinson's disease substantia nigra pars compacta reveals impairment of ubiquitin-proteasome subunits, SKP1A, aldehyde dehydrogenase, and chaperone HSC-70. Ann. N. Y. Acad. Sci. 2005, 1053:356-375.
77. Marcus D.L., Thomas C., Rodriguez C., Simberkoff K., Tsai J.S., Strafaci J.A., Freedman M.L. Increased peroxidation and reduced antioxidant enzyme activity in Alzheimer's disease. Exp. Neurol. 1998, 150:40-44.
78. Martin C.L., Duvall J.A., Ilkin Y., Simon J.S., Arreaza M.G., Wilkes K., Alvarez-Retuerto A., Whichello A., Powell C.M., Rao K., Cook E., Geschwind D.H. Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am. J. Med. Genet. B Neuropsychiatr. Genet. 2007, 144B:869-876.
79. Maruszak A., Safranow K., Gustaw K., Kijanowska-Haładyna B., Jakubowska K., Olszewska M., Styczyńska M., Berdyński M., Tysarowski A., Chlubek D., Siedlecki J., Barcikowska M., Zekanowski C. PIN1 gene variants in Alzheimer's disease. BMC Med. Genet. 2009, 10:115.
80. Matlin A.J., Clark F., Smith C.W. Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 2005, 6:386-398.
81. Meinke D.W., Cherry J.M., Dean C., Rounsley S.D., Koornneef M. Arabidopsis thaliana: a model plant for genome analysis. Science 1998, 282:662-682.
82. Mockler T.C., Chan S., Sundaresan A., Chen H., Jacobsen S.E., Ecker J.R. Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005, 85:1-15.
83. Modrek B., Lee C. A genomic view of alternative splicing. Nat. Genet. 2002, 30:13-19.
84. Mukherji M., Brill L.M., Ficarro S.B., Hampton G.M., Schultz P.G. A phosphoproteomic analysis of the ErbB2 receptor tyrosine kinase signaling pathways. Biochemistry 2006, 45:15529-15540.
85. Nagy Z. The last neuronal division: a unifying hypothesis for the pathogenesis of Alzheimer's disease. J. Cell. Mol. Med. 2005, 9:531-541.
86. Noble W., Olm V., Takata K., Casey E., Mary O., Meyerson J., Gaynor K., LaFrancois J., Wang L., Kondo T., Davies P., Burns M., Veeranna, Nixon R., Dickson D., Matsuoka Y., Ahlijanian M., Lau L.F., Duff K. Cdk5 is a key factor in tau aggregation and tangle formation in vivo. Neuron 2003, 38:555-565. 10.1016/S0896-6273(03)00259-9.
87. Nuytemans K., Meeus B., Crosiers D., Brouwers N., Goossens D., Engelborghs S., Pals P., Pickut B., Van den Broeck M., Corsmit E., Cras P., De Deyn P.P., Del-Favero J., Van Broeckhoven C., Theuns J. Relative contribution of simple mutations vs. copy number variations in five Parkinson disease genes in the Belgian population. Hum. Mutat. 2009, 30:1054-1061.
88. Okoniewski M.J., Hey Y., Pepper S.D., Miller C.J. High correspondence between Affymetrix exon and standard expression arrays. Biotechniques 2007, 42:181-185.
89. Orr H.T., Zoghbi H.Y. Trinucleotide repeats disorders. Annu. Rev. Neurosci. 2007, 30:575-621.
90. Pan Q., Bakowski M.A., Morris Q., Zhang W., Frey B.J., Hughes T.R., Blencowe B.J. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 2005, 21:73-77.
91. Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008, 40:1413-1415.
92. Pankratz N., Kissell D.K., Pauciulo M.W., Halter C.A., Rudolph A., Pfeiffer R.F., Marder K.S., Foroud T., Nichols W.C. Parkin dosage mutations have greater pathogenicity in familial PD than simple sequence mutations. Neurology 2009, 73:279-286.
93. Pericak-Vance M.A., Bebout J.L., Gaskell P.C., Yamaoka L.H., Hung W.Y., Alberts M.J., Walker A.P., Bartlett R.J., Haynes C.A., Welsh K.A., et al. Linkage studies in familial Alzheimer disease: evidence for chromosome 19 linkage. Am. J. Hum. Genet. 1991, 48:1034-1050.
94. Pigullo S., De Luca A., Barone P., Marchese R., Bellone E., Colosimo A., Scaglione C., Martinelli P., Di Maria E., Pizzuti A., Abbruzzese G., Dallapiccola B., Ajmar F., Mandich P. Mutational analysis of parkin gene by denaturing high-performance liquid chromatography (DHPLC) in essential tremor. Parkinsonism Relat. Disord. 2004, 10:357-362.
95. Plassman B.L., Langa K.M., Fisher G.G., Heeringa S.G., Weir D.R., Ofstedal M.B., Burke J.R., Hurd M.D., Potter G.G., Rodgers W.L., Steffens D.C., Willis R.J., Wallace R.B. Prevalence of dementia in the United States: the aging, demographics, and memory study. Neuroepidemiology 2007, 29:125-132.
96. Polymeropoulos M.H., Lavedan C., Leroy E., Ide S.E., Dehejia A., Dutra A., Pike B., Root H., Rubenstein J., Boyer R., Stenroos E.S., Chandrasekharappa S., Athanassiadou A., Papapetropoulos T., Johnson W.G., Lazzarini A.M., Duvoisin R.C., Di Iorio G., Golbe L.I., Nussbaum R.L. Mutation in the alpha-synuclein gene identified in families with Parkinson's disease. Science 1997, 276:2045-2047.
97. Ponte P., Gonzalez-DeWhitt P., Schilling J., Miller J., Hsu D., Greenberg B., Davis K., Wallace W., Lieberburg I., Fuller F. A new A4 amyloid mRNA contains a domain homologous to serine proteinase inhibitors. Nature 1988, 331:525-527.
98. Price D.L., Sisodia S.S. Mutant genes in familial Alzheimer's disease and transgenic models. Annu. Rev. Neurosci. 1998, 21:479-505.
99. Rademakers R., Cruts M., van Broeckhoven C. The role of tau (MAPT) in frontotemporal dementia and related tauopathies. Hum. Mutat. 2004, 24:277-295.
100. Ranum L.P., Cooper T.A. RNA-mediated neuromuscular disorders. Annu. Rev. Neurosci. 2006, 29:259-277.
101. Raschetti R., Albanese E., Vanacore N., Maggini M. Cholinesterase inhibitors in mild cognitive impairment: a systematic review of randomised trials. PLoS Med. 2007, 4:e338.
102. Reiner A., Albin R.L., Anderson K.D., D'Amato C.J., Penney J.B., Young A.B. Differential loss of striatal projection neurons in Huntington disease. Proc. Natl. Acad. Sci. U. S. A. 1988, 85:5733-5737.
103. Rockenstein E.M., McConlogue L., Tan H., Power M., Masliah E., Mucke L. Levels and alternative splicing of amyloid beta protein precursor (APP) transcripts in brains of APP transgenic mice and humans with Alzheimer's disease. J. Biol. Chem. 1995, 270:28257-28267.
104. Sato N., Hori O., Yamaguchi A., Lambert J.C., Chartier-Harlin M.C., Robinson P.A., Delacourte A., Schmidt A.M., Furuyama T., Imaizumi K., Tohyama M., Takagi T. A novel presenilin-2 splice variant in human Alzheimer's disease brain tissue. J. Neurochem. 1999, 72:2498-2505.
105. Schadt E.E., Linderman M.D., Sorenson J., Lee L., Nolan G.P. Computational solutions to large-scale data management and analysis. Nat. Rev. Genet. 2010, 11:647-657.
106. Scherfler C., Khan N.L., Pavese N., Eunson L., Graham E., Lees A.J., Quinn N.P., Wood N.W., Brooks D.J., Piccini P.P. Striatal and cortical pre- and postsynaptic dopaminergic dysfunction in sporadic parkin-linked parkinsonism. Brain 2004, 127:1332-1342.
107. Sebat J., Lakshmi B., Malhotra D., Troge J., Lese-Martin C., Walsh T., Yamrom B., Yoon S., Krasnitz A., Kendall J., Leotta A., Pai D., Zhang R., Lee Y.H., Hicks J., Spence S.J., Lee A.T., Puura K., Lehtimäki T., Ledbetter D., Gregersen P.K., Bregman J., Sutcliffe J.S., Jobanputra V., Chung W., Warburton D., King M.C., Skuse D., Geschwind D.H., Gilliam T.C., Ye K., Wigler M. Strong association of de novo copy number mutations with autism. Science 2007, 316:445-449.
108. Shehadeh L.A., Yu K., Wang L., Guevara A., Singer C., Vance J., Papapetropoulos S. SRRM2, a potential blood biomarker revealing high alternative splicing in Parkinson's disease. PLoS One 2010, 5:e9104.
109. Shendure J., Ji H. Next-generation DNA sequencing. Nat. Biotechnol. 2008, 26:1135-1145.
110. Shepherd C., McCann H., Halliday G.M. Variations in the neuropathology of familial Alzheimer's disease. Acta Neuropathol. 2009, 118:37-52.
111. Shobab L.A., Hsiung G.Y., Feldman H.H. Cholesterol in Alzheimer's disease. Lancet Neurol. 2005, 4:841-852. 10.1016/S1474-4422(05)70248-9.
112. Singleton A.B., Hall R., Ballard C.G., Perry R.H., Xuereb J.H., Rubinsztein D.C., Tysoe C., Matthews P., Cordell B., Kumar-Singh S., De Jonghe C., Cruts M., van Broeckhoven C., Morris C.M. Pathology of early-onset Alzheimer's disease cases bearing the Thr113-114ins presenilin-1 mutation. Brain 2000, 123:2467-2474.
113. Sinha S., Anderson J.P., Barbour R., Basi G.S., Caccavello R., Davis D., Doan M., Dovey H.F., Frigon N., Hong J., Jacobson-Croak K., Jewett N., Keim P., Knops J., Lieberburg I., Power M., Tan H., Tatsuno G., Tung J., Schenk D., Seubert P., Suomensaari S.M., Wang S., Walker D., Zhao J., McConlogue L., John V. Purification and cloning of amyloid precursor protein beta-secretase from human brain. Nature 1999, 402:537-540.
114. Sipione S., Cattaneo E. Modeling Huntington's disease in cells, flies, and mice. Mol. Neurobiol. 2001, 23:21-51. 10.1385/MN:23:1:21.
115. Smith A.D., Xuan Z., Zhang M.Q. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinform. 2008, 9:128.
116. Smith P., Al Hashimi A., Girard J., Delay C., Hébert S.S. In vivo regulation of amyloid precursor protein neuronal splicing by microRNAs. J. Neurochem. 2011, 116:240-247.
117. Spillantini M.G., Murrell J.R., Goedert M., Farlow M.R., Klug A., Ghetti B. Mutation in the tau gene in familial multiple system tauopathy with presenile dementia. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:7737-7741.
118. Spillantini M.G., Schmidt M.L., Lee V.M., Trojanowski J.Q., Jakes R., Goedert M. Alpha-synuclein in Lewy bodies. Nature 1997, 388:839-840.
119. Sudmant P.H., Kitzman J.O., Antonacci F., Alkan C., Malig M., Tsalenko A., Sampas N., Bruhn L., Shendure J., Eichler E.E. Diversity of human copy number variation and multicopy genes. Science 2010, 330:641-646.
120. Sunada Y., Saito F., Matsumura K., Shimizu T. Differential expression of the parkin gene in the human brain and peripheral leukocytes. Neurosci. Lett. 1998, 254:180-182. 10.1016/S0304-3940(98)00697-1.
121. Sutherland G.T., Janitz M., Kril J.J. Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics?. J. Neurochem. 2011, 116:937-946.
122. Sze C.I., Bi H., Kleinschmidt-DeMasters B.K., Filley C.M., Martin L.J. Selective regional loss of exocytotic presynaptic vesicle proteins in Alzheimer's disease brains. J. Neurol. Sci. 2000, 175:81-90. 10.1016/S0022-510X(00)00285-9.
123. Tan E.K., Shen H., Tan J.M., Lim K.L., Fook-Chong S., Hu W.P., Paterson M.C., Chandran V.R., Yew K., Tan C., Yuen Y., Pavanni R., Wong M.C., Puvan K., Zhao Y. Differential expression of splice variant and wild-type parkin in sporadic Parkinson's disease. Neurogenetics 2005, 6:179-184.
124. Tanahashi H., Tabira T. Three novel alternatively spliced isoforms of the human beta-site amyloid precursor protein cleaving enzyme (BACE) and their effect on amyloid beta-peptide production. Neurosci. Lett. 2001, 307:9-12. 10.1016/S0304-3940(01)01912-7.
125. Tang K., Wang C., Shen C., Sheng S., Ravid R., Jing N. Identification of a novel alternative splicing isoform of human amyloid precursor protein gene, APP639. Eur. J. Neurosci. 2003, 18:102-108.
126. Tanzi R.E., Wenniger J.J., Hyman B.T. Cellular specificity and regional distribution of amyloid beta protein precursor alternative transcripts are unaltered in Alzheimer hippocampal formation. Brain Res. Mol. Brain Res. 1993, 18:246-252.
127. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group. Cell 1993, 72:971-983. The Huntington's Disease Collaborative Research Group. 10.1016/0092-8674(93)90585-E.
128. Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
129. Twine N.A., Janitz K., Wilkins M.R., Janitz M. Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. PLoS One 2011, 6:e16266.
130. Tysoe C., Whittaker J., Xuereb J., Cairns N.J., Cruts M., Van Broeckhoven C., Wilcock G., Rubinsztein D.C. A presenilin-1 truncating mutation is present in two cases with autopsy-confirmed early-onset Alzheimer disease. Am. J. Hum. Genet. 1998, 62:70-76.
131. Vinciguerra P., Stutz F. mRNA export: an assembly line from genes to nuclear pores. Curr. Opin. Cell Biol. 2004, 16:285-292.
132. Vives-Bauza C., Zhou C., Huang Y., Cui M., de Vries R.L., Kim J., May J., Tocilescu M.A., Liu W., Ko H.S., Magrané J., Moore D.J., Dawson V.L., Grailhe R., Dawson T.M., Li C., Tieu K., Przedborski S. PINK1-dependent recruitment of Parkin to mitochondria in mitophagy. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:378-383.
133. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
134. West A.B., Maidment N.T. Genetics of parkin-linked disease. Hum. Genet. 2004, 114:327-336.
135. West A.B., Maraganore D., Crook J., Lesnick T., Lockhart P.J., Wilkes K.M., Kapatos G., Hardy J.A., Farrer M.J. Functional association of the parkin gene promoter with idiopathic Parkinson's disease. Hum. Mol. Genet. 2002, 11:2787-2792.
136. Wyss-Coray T. Inflammation in Alzheimer disease: driving force, bystander or beneficial response?. Nat. Med. 2006, 12:1005-1015.
137. Xing Y., Lee C. Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet. 2006, 7:499-509.
138. Xu P.T., Gilbert J.R., Qiu H.L., Ervin J., Rothrock-Christian T.R., Hulette C., Schmechel D.E. Specific regional transcription of apolipoprotein E in human brain neurons. Am. J. Pathol. 1999, 154:601-611. 10.1016/S0002-9440(10)65305-9.
139. Yeo G., Holste D., Kreiman G., Burge C.B. Variation in alternative splicing across human tissues. Genome Biol. 2004, 5:R74.
140. Zarranz J.J., Alegre J., Gómez-Esteban J.C., Lezcano E., Ros R., Ampuero I., Vidal L., Hoenicka J., Rodriguez O., Atarés B., Llorens V., Gomez Tortosa E., del Ser T., Muñoz D.G., de Yebenes J.G. The new mutation, E46K, of alpha-synuclein causes Parkinson and Lewy body dementia. Ann. Neurol. 2004, 55:164-173.
141. Zhang C., Li H.R., Fan J.B., Wang-Rodriguez J., Downs T., Fu X.D., Zhang M.Q. Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinform. 2006, 7:202.
142. Zuccato C., Ciammola A., Rigamonti D., Leavitt B.R., Goffredo D., Conti L., MacDonald M.E., Friedlander R.M., Silani V., Hayden M.R., Timmusk T., Sipione S., Cattaneo E. Loss of huntingtin-mediated BDNF gene transcription in Huntington's disease. Science 2001, 293:493-498.
143. Zuccato C., Liber D., Ramos C., Tarditi A., Rigamonti D., Tartari M., Valenza M., Cattaneo E. Progressive loss of BDNF in a mouse model of Huntington's disease and rescue by BDNF delivery. Pharmacol. Res.s 2005, 52:133-139.