Identification and characterization of novel splice variants of the human EPM2A gene mutated in Lafora progressive myoclonus epilepsy

Genomics

Volumn 99, Issue 1, 2012, Pages 36-43

  Dubey, Deepti ^a   Parihar, Rashmi ^a   Ganesh, Subramaniam ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY KANPUR   (India)

Author keywords

Alternative splicing; Epilepsy; Phosphatase; Protein diversity

Indexed keywords

DUAL SPECIFICITY PHOSPHATASE; LAFORIN; RNA; UBIQUITIN PROTEIN LIGASE; UNCLASSIFIED DRUG;

ALTERNATIVE RNA SPLICING; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL FUNCTION; CELL LINE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; EPM2A GENE; GENE; GENE EXPRESSION; GENE IDENTIFICATION; GENE MUTATION; GENETIC REGULATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN TISSUE; MOUSE; MYOCLONUS EPILEPSY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN INTERACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION;

ALTERNATIVE SPLICING; ANIMALS; CARRIER PROTEINS; CELL LINE; DIMERIZATION; GLYCOGEN; HUMANS; ISOENZYMES; LAFORA DISEASE; MICE; MUTATION; PROTEIN TYROSINE PHOSPHATASES, NON-RECEPTOR;

EID: 84855199805     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.10.001     Document Type: Article

References (34)

1. Ganesh S., Puri R., Singh S., Mittal S., Dubey D. Recent advances in the molecular basis of Lafora's progressive myoclonus epilepsy. J. Hum. Genet. 2006, 51:1-8.
2. Singh S., Ganesh S. Lafora progressive myoclonus epilepsy: a meta-analysis of reported mutations in the first decade following the discovery of the EPM2A and NHLRC1 genes. Hum. Mutat. 2009, 30:715-723.
3. Chan E.M., Young E.J., Ianzano L., Munteanu I., Zhao X., Christopoulos C.C., et al. Mutations in NHLRC1 cause progressive myoclonus epilepsy. Nat. Genet. 2003, 35:125-127.
4. Gentry M.S., Worby C.A., Dixon J.E. Insights into Lafora disease: malin is an E3 ubiquitin ligase that ubiquitinates and promotes the degradation of laforin. Proc. Natl Acad. Sci. USA 2005, 102:8501-8506.
5. Garyali P., Siwach P., Singh P.K., Puri R., Mittal S., Sengupta S., Parihar R., Ganesh S. The malin-laforin complex suppresses the cellular toxicity of misfolded proteins by promoting their degradation through the ubiquitin-proteasome system. Hum. Mol. Genet. 2009, 18:688-700.
6. Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
7. Hartmann B., Valcárcel J. Decrypting the genome's alternative messages. Curr. Opin. Cell Biol. 2009, 21:377-386.
8. Ganesh S., Suzuki T., Yamakawa K. Alternative splicing modulates subcellular localization of laforin. Biochem. Biophys. Res. Commun. 2002, 291:1134-1137.
9. Ianzano L., Young E.J., Zhao X.C., Chan E.M., Rodriguez M.T., Torrado M.V., et al. Loss of function of the cytoplasmic isoform of the protein laforin (EPM2A) causes Lafora progressive myoclonus epilepsy. Hum. Mutat. 2004, 23:170-176.
10. Dubey D., Ganesh S. Modulation of functional properties of laforin phosphatase by alternative splicing reveals a novel mechanism for the EPM2A gene in Lafora progressive myoclonus epilepsy. Hum. Mol. Genet. 2008, 17:3010-3020.
11. Ganesh S., Tsurutani N., Suzuki T., Hoshii Y., Ishihara T., Delgado-Escueta A.V., Yamakawa K. The carbohydrate-binding domain of Lafora disease protein targets Lafora polyglucosan bodies. Biochem. Biophys. Res. Commun. 2004, 313:1101-1109.
12. Graveley B.R. Sorting out the complexity of SR protein functions. RNA 2000, 6:1197-1211.
13. Cartegni L., Wang J., Zhu Z., Zhang M.Q., Krainer A.R. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res. 2003, 31:3568-3571.
14. Nishikawa T., Ota T., Isogai T. Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences. Bioinformatics 2000, 16:960-967.
15. Rigou P., Piddubnyak V., Faye A., Rain J.C., Michel L., Calvo F., Poyet J.L. The antiapoptotic protein AAC-11 interacts with and regulates Acinus-mediated DNA fragmentation. EMBO J. 2009, 28:1576-1588.
16. Ganesh S., Agarwala K.L., Ueda K., Akagi T., Shoda K., Usui T., et al. Laforin, defective in the progressive myoclonus epilepsy of Lafora type, is a dual-specificity phosphatase associated with polyribosomes. Hum. Mol. Genet. 2000, 9:2251-2261.
17. Minassian B.A., Lee J.R., Herbrick J.A., Huizenga J., Soder S., Mungall A.J., et al. Mutations in a gene encoding a novel protein tyrosine phosphatase cause progressive myoclonus epilepsy. Nat. Genet. 1998, 20:171-174.
18. Serratosa J.M., Gómez-Garre P., Gallardo M.E., Anta B., de Bernabé D.B., Lindhout D., et al. A novel protein tyrosine phosphatase gene is mutated in progressive myoclonus epilepsy of the Lafora type (EPM2). Hum. Mol. Genet. 1999, 8:345-352.
19. Ganesh S., Shoda K., Amano K., Uchiyama A., Kumada S., Moriyama N., et al. Mutation screening for Japanese Lafora's disease patients: identification of novel sequence variants in the coding and upstream regulatory regions of EPM2A gene. Mol. Cell. Probes 2001, 15:281-289.
20. Ayoubi T.A., Van De Ven W.J. Regulation of gene expression by alternative promoters. FASEB J. 1996, 10:453-460.
21. Liang H., Landweber L.F. A genome-wide study of dual coding regions in human alternatively spliced genes. Genome Res. 2006, 16:190-196.
22. Quelle D.E., Zindy F., Ashmun R.A., Sherr C.J. Alternative reading frames of the INK4a tumor suppressor gene encode two unrelated proteins capable of inducing cell cycle arrest. Cell 1995, 83:993-1000.
23. Labarrière N., Selvais P.L., Lemaigre F.P., Michel A., Maiter D.M., Rousseau G.G. A novel transcriptional activator originating from an upstream promoter in human growth hormone gene. J. Biol. Chem. 1995, 270:19205-19208.
24. Guittaut M., Charpentier S., Normand T., Dubois M., Raimond J., Legrand A. Identification of an internal gene to the human Galectin-3 gene with two different overlapping reading frames that do not encode Galectin-3. J. Biol. Chem. 2001, 276:2652-2657.
25. Stallmeyer B., Drugeon G., Reiss J., Haenni A.L., Mendel R.R. Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames. Am. J. Hum. Genet. 1999, 64:698-705.
26. Klemke M., Kehlenbach R.H., Huttner W.B. Two overlapping reading frames in a single exon encode interacting proteins-a novel way of gene usage. EMBO J. 2001, 20:3849-3860.
27. Yoshida H., Matsui T., Yamamoto A., Okada T., Mori K. XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. Cell 2001, 107:881-891.
28. Poulin F., Brueschke A., Sonenberg N. Gene fusion and overlapping reading frames in the mammalian genes for 4E-BP3 and MASK. J. Biol. Chem. 2003, 278:52290-52297.
29. Gray N.K., Wickens M. Control of translation initiation in animals. Annu. Rev. Cell Dev. Biol. 1998, 14:399-458.
30. Wu W., Baxter J.E., Wattam S.L., Hayward D.G., Fardilha M., Knebel A., et al. Alternative splicing controls nuclear translocation of the cell cycle-regulated Nek2 kinase. J. Biol. Chem. 2007, 282:26431-26440.
31. Bult A., Zhao F., Dirkx R., Raghunathan A., Solimena M., Lombroso P.J. STEP: a family of brain-enriched PTPs. Alternative splicing produces transmembrane, cytosolic and truncated isoforms. Eur. J. Cell Biol. 1997, 72:337-344.
32. Aoyama K., Matsuda T., Aoki N. Characterization of newly identified four isoforms for a putative cytosolic protein tyrosine phosphatase PTP36. Biochem. Biophys. Res. Commun. 1999, 266:523-531.
33. Ganesh S., Delgado-Escueta A.V., Suzuki T., Francheschetti S., Riggio C., Avanzini G., et al. Genotype-phenotype correlations for EPM2A mutations in Lafora's progressive myoclonus epilepsy: exon 1 mutations associate with an early-onset cognitive deficit subphenotype. Hum. Mol. Genet. 2002, 11:1263-1271.
34. Annesi G., Sofia V., Gambardella A., Candiano I.C., Spadafora P., Annesi F., Cutuli N., De Marco E.V., Civitelli D., Carrideo S., Tarantino P., Barone R., Zappia M., Quattrone A. A novel exon 1 mutation in a patient with atypical Lafora progressive myoclonus epilepsy seen as childhood-onset cognitive deficit. Epilepsia 2004, 45:294-295.