Analysis of novel NEFL mRNA targeting microRNAs in amyotrophic lateral sclerosis

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Ishtiaq, Muhammad ^a   Campos Melo, Danae ^a   Volkening, Kathryn ^a,b   Strong, Michael J ^a,b  

^a ROBARTS RESEARCH INSTITUTE   (Canada)

^b WESTERN UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA B1336; MICRORNA B2403; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FUNCTIONAL ASSESSMENT; GENE; GENE LIBRARY; GENE SILENCING; GENE TARGETING; GENETIC STABILITY; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MOLECULAR WEIGHT; NEFL GENE; NEUROFILAMENT; PATHOGENESIS; PROTEIN PROCESSING; REAL TIME POLYMERASE CHAIN REACTION; RNA TRANSLATION; SPINAL CORD; STEADY STATE;

3' UNTRANSLATED REGIONS; AGED; AMYOTROPHIC LATERAL SCLEROSIS; FEMALE; GENE EXPRESSION; HEK293 CELLS; HUMANS; INVERTED REPEAT SEQUENCES; MALE; MICRORNAS; MIDDLE AGED; MODELS, MOLECULAR; MUTATION; NEUROFILAMENT PROTEINS; NUCLEIC ACID CONFORMATION; RESPONSE ELEMENTS; RNA INTERFERENCE; SPINAL CORD;

EID: 84898606538     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085653     Document Type: Article

References (57)

1. Zeller JL, Lynm C, Glass RM (2007) JAMA patient page. Amyotrophic lateral sclerosis. JAMA 298: 248.
2. Strong MJ, Kesavapany S, Pant HC (2005) The pathobiology of amyotrophic lateral sclerosis: a proteinopathy? J Neuropathol Exp Neurol 64: 649-664. (Pubitemid 41177106)
3. Al-Chalabi A, Jones A, Troakes C, King A, Al-Sarraj S, et al. (2012) The genetics and neuropathology of amyotrophic lateral sclerosis. Acta Neuropathol 124: 339-352.
4. Kondo A, Iwaki T, Tateishi J, Kirimoto K, Morimoto T, et al. (1986) Accumulation of neurofilaments in a sporadic case of amyotrophic lateral sclerosis. Jpn J Psychiatry Neurol 40: 677-684. (Pubitemid 17050629)
5. Arai T, Hasegawa M, Akiyama H, Ikeda K, Nonaka T, et al. (2006) TDP-43 is a component of ubiquitin-positive tau-negative inclusions in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Biochem Biophys Res Commun 351: 602-611. (Pubitemid 44708852)
6. Neumann M, Sampathu DM, Kwong LK, Truax AC, Micsenyi MC, et al. (2006) Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science 314: 130-133. (Pubitemid 44547757)
7. Kwiatkowski TJ Jr., Bosco DA, Leclerc AL, Tamrazian E, Vanderburg CR, et al. (2009) Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis. Science 323: 1205-1208.
8. Vance C, Rogelj B, Hortobagyi T, De Vos KJ, Nishimura AL, et al. (2009) Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science 323: 1208-1211.
9. Droppelmann CA, Keller BA, Campos-Melo D, Volkening K, Strong MJ (2013) Rho guanine nucleotide exchange factor is an NFL mRNA destabilizing factor that forms cytoplasmic inclusions in amyotrophic lateral sclerosis. Neurobiol Aging 34: 248-262.
10. Bergeron C, Beric-Maskarel K, Muntasser S, Weyer L, Somerville MJ, et al. (1994) Neurofilament light and polyadenylated mRNA levels are decreased in amyotrophic lateral sclerosis motor neurons. J Neuropathol Exp Neurol 53: 221-230. (Pubitemid 24146859)
11. Wong NK, He BP, Strong MJ (2000) Characterization of neuronal intermediate filament protein expression in cervical spinal motor neurons in sporadic amyotrophic lateral sclerosis (ALS). J Neuropathol Exp Neurol 59: 972-982.
12. Ge WW, Leystra-Lantz C, Wen W, Strong MJ (2003) Selective loss of transacting instability determinants of neurofilament mRNA in amyotrophic lateral sclerosis spinal cord. J Biol Chem 278: 26558-26563. (Pubitemid 36876799)
13. Menzies FM, Grierson AJ, Cookson MR, Heath PR, Tomkins J, et al. (2002) Selective loss of neurofilament expression in Cu/Zn superoxide dismutase (SOD1) linked amyotrophic lateral sclerosis. J Neurochem 82: 1118-1128. (Pubitemid 34966624)
14. Strong MJ (2010) The evidence for altered RNA metabolism in amyotrophic lateral sclerosis (ALS). J Neurol Sci 288: 1-12.
15. Ge WW, Volkening K, Leystra-Lantz C, Jaffe H, Strong MJ (2007) 14-3-3 protein binds to the low molecular weight neurofilament (NFL) mRNA 39 UTR. Mol Cell Neurosci 34: 80-87. (Pubitemid 46026930)
16. Strong MJ, Volkening K, Hammond R, Yang W, Strong W, et al. (2007) TDP43 is a human low molecular weight neurofilament (hNFL) mRNA-binding protein. Mol Cell Neurosci 35: 320-327. (Pubitemid 46843567)
17. Volkening K, Leystra-Lantz C, Strong MJ (2010) Human low molecular weight neurofilament (NFL) mRNA interacts with a predicted p190RhoGEF homologue (RGNEF) in humans. Amyotroph Lateral Scler 11: 97-103.
18. Ge WW, Wen W, Strong W, Leystra-Lantz C, Strong MJ (2005) Mutant copper-zinc superoxide dismutase binds to and destabilizes human low molecular weight neurofilament mRNA. J Biol Chem 280: 118-124. (Pubitemid 40164972)
19. Volkening K, Leystra-Lantz C, Yang W, Jaffee H, Strong MJ (2009) Tar DNA binding protein of 43 kDa (TDP-43), 14-3-3 proteins and copper/zinc superoxide dismutase (SOD1) interact to modulate NFL mRNA stability. Implications for altered RNA processing in amyotrophic lateral sclerosis (ALS). Brain Res 1305: 168-182.
20. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864. (Pubitemid 33032105)
21. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854. (Pubitemid 24014542)
22. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862. (Pubitemid 33032104)
23. Cerutti H, Ma X, Msanne J, Repas T (2011) RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function. Eukaryot Cell 10: 1164-1172.
24. Crippa S, Cassano M, Sampaolesi M (2012) Role of miRNAs in muscle stem cell biology: proliferation, differentiation and death. Curr Pharm Des 18: 1718-1729.
25. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. (2003) A uniform system for microRNA annotation. RNA 9: 277-279. (Pubitemid 36246165)
26. Ghosh T, Soni K, Scaria V, Halimani M, Bhattacharjee C, et al. (2008) MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene. Nucleic Acids Res 36: 6318-6332.
27. Shimakami T, Yamane D, Jangra RK, Kempf BJ, Spaniel C, et al. (2012) Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex. Proc Natl Acad Sci U S A 109: 941-946.
28. Orom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 59UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30: 460-471. (Pubitemid 351672378)
29. Kucherenko MM, Barth J, Fiala A, Shcherbata HR (2012) Steroid-induced microRNA let-7 acts as a spatio-temporal code for neuronal cell fate in the developing Drosophila brain. EMBO J 31: 4511-4523.
30. Sonntag KC (2010) MicroRNAs and deregulated gene expression networks in neurodegeneration. Brain Res 1338: 48-57.
31. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, et al. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24. (Pubitemid 40094599)
32. Berezikov E, Cuppen E, Plasterk RH (2006) Approaches to microRNA discovery. Nat Genet 38 SUPPL.: S2-7.
33. Tyagi S, Vaz C, Gupta V, Bhatia R, Maheshwari S, et al. (2008) CID-miRNA: a web server for prediction of novel miRNA precursors in human genome. Biochem Biophys Res Commun 372: 831-834.
34. Ritchie W, Theodule FX, Gautheret D (2008) Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 24: 1394-1396. (Pubitemid 351737146)
35. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)
36. Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36: D149-153. (Pubitemid 351149712)
37. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
38. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798. (Pubitemid 38058492)
39. Ellwanger DC, Buttner FA, Mewes HW, Stumpflen V (2011) The sufficient minimal set of miRNA seed types. Bioinformatics 27: 1346-1350.
40. Campos-Melo D, Droppelmann CA, He Z, Volkening K, Strong MJ (2013) Altered microRNA expression profile in Amyotrophic Lateral Sclerosis: A role in the regulation of NFL mRNA levels. Mol Brain 6: 26.
41. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of posttranscriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9: 102-114.
42. Eulalio A, Schulte L, Vogel J (2012) The mammalian microRNA response to bacterial infections. RNA Biol 9: 742-750.
43. O'Carroll D, Schaefer A (2013) General principals of miRNA biogenesis and regulation in the brain. Neuropsychopharmacology 38: 39-54.
44. Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, et al. (2009) miR- 145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460: 705-710.
45. Bhattacharyya SN, Filipowicz W (2007) Argonautes and company: sailing against the wind. Cell 128: 1027-1028. (Pubitemid 46427878)
46. Saraiya AA, Li W, Wang CC (2013) Transition of a microRNA from repressing to activating translation depending on the extent of base pairing with the target. PLoS One 8: e55672.
47. Buchan JR, Parker R (2007) Molecular biology. The two faces of miRNA. Science 318: 1877-1878.
48. Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318: 1931-1934.
49. Iwasaki S, Tomari Y (2009) Argonaute-mediated translational repression (and activation). Fly (Austin) 3: 204-206.
50. Lee S, Vasudevan S (2013) Post-transcriptional stimulation of gene expression by microRNAs. Adv Exp Med Biol 768: 97-126.
51. Williams AH, Valdez G, Moresi V, Qi X, McAnally J, et al. (2009) MicroRNA- 206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science 326: 1549-1554.
52. Haramati S, Chapnik E, Sztainberg Y, Eilam R, Zwang R, et al. (2010) miRNA malfunction causes spinal motor neuron disease. Proc Natl Acad Sci U S A 107: 13111-13116.
53. Shioya M, Obayashi S, Tabunoki H, Arima K, Saito Y, et al. (2010) Aberrant microRNA expression in the brains of neurodegenerative diseases: miR-29a decreased in Alzheimer disease brains targets neurone navigator 3. Neuropathol Appl Neurobiol 36: 320-330.
54. De Felice B, Guida M, Coppola C, De Mieri G, Cotrufo R (2012) A miRNA signature in leukocytes from sporadic amyotrophic lateral sclerosis. Gene 508: 35-40.
55. Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20: 2911-2917. (Pubitemid 39619182)
56. Ebert MS, Sharp PA (2010) Emerging roles for natural microRNA sponges. Curr Biol 20: R858-861.
57. Fowler A, Thomson D, Giles K, Maleki S, Mreich E, et al. (2011) miR-124a is frequently down-regulated in glioblastoma and is involved in migration and invasion. Eur J Cancer 47: 953-963.