Defining larger roles for "tiny" RNA molecules: Role of miRNAs in neurodegeneration research

Journal of Neuroimmune Pharmacology

Volumn 5, Issue 1, 2010, Pages 63-69

  Yelamanchili, Sowmya V ^a   Fox, Howard S ^a  

^a NEBRASKA MEDICAL CENTER   (United States)

Author keywords

Gene array; HIV; MicroRNA; MRNA; Neurodegeneration; Neuron; Transcriptional regulation; Translational regulation

Indexed keywords

MICRORNA;

GENE IDENTIFICATION; GENE ISOLATION; HUMAN; MEDICAL RESEARCH; NERVE DEGENERATION; NEUROSCIENCE; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION;

ANIMALS; BRAIN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; NERVE DEGENERATION; NEURODEGENERATIVE DISEASES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 77249143447     PISSN: 15571890     EISSN: 15571904     Source Type: Journal    
DOI: 10.1007/s11481-009-9172-4     Document Type: Review

References (66)

1. D Baek J Villen C Shin FD Camargo SP Gygi DP Bartel 2008 The impact of microRNAs on protein output Nature 455 64 71 10.1038/nature07242 18668037
2. C Barbato I Arisi ME Frizzo R Brandi L Da Sacco A Masotti 2009 Computational challenges in miRNA target predictions: to be or not to be a true target? J Biomed Biotechnol 2009 803069 19551154
3. I Bentwich A Avniel Y Karov R Aharonov S Gilad O Barad A Barzilai P Einat U Einav E Meiri E Sharon Y Spector Z Bentwich 2005 Identification of hundreds of conserved and nonconserved human microRNAs Nat Genet 37 766 770 10.1038/ng1590 15965474 (Pubitemid 41754896)
4. E Berezikov V Guryev J van de Belt E Wienholds RH Plasterk E Cuppen 2005 Phylogenetic shadowing and computational identification of human microRNA genes Cell 120 21 24 10.1016/j.cell.2004.12.031 15652478 (Pubitemid 40094599)
5. E Berezikov E Cuppen RH Plasterk 2006 Approaches to microRNA discovery Nat Genet 38 Suppl S2 S7 10.1038/ng1794 16736019 (Pubitemid 43920936)
6. V Boissonneault I Plante S Rivest P Provost 2009 MicroRNA-298 and microRNA-328 regulate expression of mouse beta-amyloid precursor protein-converting enzyme 1 J Biol Chem 284 1971 1981 10.1074/jbc.M807530200 18986979
7. GM Borchert W Lanier BL Davidson 2006 RNA polymerase III transcribes human microRNAs Nat Struct Mol Biol 13 1097 1101 10.1038/nsmb1167 17099701 (Pubitemid 44885920)
8. X Cai CH Hagedorn BR Cullen 2004 Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs RNA 10 1957 1966 10.1261/rna.7135204 15525708 (Pubitemid 39557833)
9. LC Cheng E Pastrana M Tavazoie F Doetsch 2009 miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche Nat Neurosci 12 399 408 10.1038/nn.2294 19287386
10. Cogswell JP, Ward J, Taylor IA, Waters M, Shi Y, Cannon B, Kelnar K, Kemppainen J, Brown D, Chen C, Prinjha RK, Richardson JC, Saunders AM, Roses AD, Richards CA 2008 Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways J Alzheimers Dis 14 27 41
11. C Conaco S Otto JJ Han G Mandel 2006 Reciprocal actions of REST and a microRNA promote neuronal identity Proc Natl Acad Sci USA 103 2422 2427 10.1073/pnas.0511041103 16461918 (Pubitemid 43271685)
12. AM Denli BB Tops RH Plasterk RF Ketting GJ Hannon 2004 Processing of primary microRNAs by the microprocessor complex Nature 432 231 235 10.1038/nature03049 15531879 (Pubitemid 39545854)
13. MR Friedlander W Chen C Adamidi J Maaskola R Einspanier S Knespel N Rajewsky 2008 Discovering microRNAs from deep sequencing data using miRDeep Nat Biotechnol 26 407 415 10.1038/nbt1394 18392026
14. J Han Y Lee KH Yeom JW Nam I Heo JK Rhee SY Sohn Y Cho BT Zhang VN Kim 2006 Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex Cell 125 887 901 10.1016/j.cell.2006.03.043 16751099 (Pubitemid 43810154)
15. SS Hebert K Horre L Nicolai AS Papadopoulou W Mandemakers AN Silahtaroglu S Kauppinen A Delacourte B De Strooper 2008 Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/beta-secretase expression Proc Natl Acad Sci USA 105 6415 6420 10.1073/pnas.0710263105 18434550 (Pubitemid 351758360)
16. SS Hebert K Horre L Nicolai B Bergmans AS Papadopoulou A Delacourte B De Strooper 2009 MicroRNA regulation of Alzheimer's amyloid precursor protein expression Neurobiol Dis 33 422 428 10.1016/j.nbd.2008.11.009 19110058
17. G Hutvagner J McLachlan AE Pasquinelli E Balint T Tuschl PD Zamore 2001 A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA Science 293 834 838 10.1126/science.1062961 11452083 (Pubitemid 32743968)
18. R Johnson C Zuccato ND Belyaev DJ Guest E Cattaneo NJ Buckley 2008 A microRNA-based gene dysregulation pathway in Huntington's disease Neurobiol Dis 29 438 445 10.1016/j.nbd.2007.11.001 18082412
19. E Junn KW Lee BS Jeong TW Chan JY Im MM Mouradian 2009 Repression of alpha-synuclein expression and toxicity by microRNA-7 Proc Natl Acad Sci USA 106 13052 13057 10.1073/pnas.0906277106 19628698
20. AA Khan D Betel ML Miller C Sander CS Leslie DS Marks 2009 Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs Nat Biotechnol 27 549 555 10.1038/nbt0709-671a 19465925
21. J Kim K Inoue J Ishii WB Vanti SV Voronov E Murchison G Hannon A Abeliovich 2007 A MicroRNA feedback circuit in midbrain dopamine neurons Science 317 1220 1224 10.1126/science.1140481 17761882
22. W Kong JJ Zhao L He JQ Cheng 2009 Strategies for profiling microRNA expression J Cell Physiol 218 22 25 10.1002/jcp.21577 18767038
23. AM Krichevsky KS King CP Donahue K Khrapko KS Kosik 2003 A microRNA array reveals extensive regulation of microRNAs during brain development RNA 9 1274 1281 10.1261/rna.5980303 13130141 (Pubitemid 37151681)
24. AM Krichevsky KC Sonntag O Isacson KS Kosik 2006 Specific microRNAs modulate embryonic stem cell-derived neurogenesis Stem Cells 24 857 864 10.1634/stemcells.2005-0441 16357340 (Pubitemid 44464719)
25. MJ Kye T Liu SF Levy NL Xu BB Groves R Bonneau K Lao KS Kosik 2007 Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR RNA 13 1224 1234 10.1261/rna.480407 17592044 (Pubitemid 47080468)
26. M Lagos-Quintana R Rauhut W Lendeckel T Tuschl 2001 Identification of novel genes coding for small expressed RNAs Science 294 853 858 10.1126/science.1064921 11679670 (Pubitemid 33032103)
27. P Landgraf, et al. 2007 A mammalian microRNA expression atlas based on small RNA library sequencing Cell 129 1401 1414 10.1016/j.cell.2007.04.040 17604727 (Pubitemid 46970709)
28. NC Lau LP Lim EG Weinstein DP Bartel 2001 An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294 858 862 10.1126/science.1065062 11679671 (Pubitemid 33032104)
29. RC Lee V Ambros 2001 An extensive class of small RNAs in Caenorhabditis elegans Science 294 862 864 10.1126/science.1065329 11679672 (Pubitemid 33032105)
30. RC Lee RL Feinbaum V Ambros 1993 The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 843 854 10.1016/0092-8674(93)90529-Y 8252621 (Pubitemid 24014542)
31. Y Lee C Ahn J Han H Choi J Kim J Yim J Lee P Provost O Radmark S Kim VN Kim 2003 The nuclear RNase III Drosha initiates microRNA processing Nature 425 415 419 10.1038/nature01957 14508493 (Pubitemid 37187272)
32. Y Lee M Kim J Han KH Yeom S Lee SH Baek VN Kim 2004 MicroRNA genes are transcribed by RNA polymerase II EMBO J 23 4051 4060 10.1038/sj.emboj.7600385 15372072 (Pubitemid 39472426)
33. Y Lee RC Samaco JR Gatchel C Thaller HT Orr HY Zoghbi 2008 miR-19, miR-101 and miR-130 co-regulate ATXN1 levels to potentially modulate SCA1 pathogenesis Nat Neurosci 11 1137 1139 10.1038/nn.2183 18758459
34. CG Liu GA Calin B Meloon N Gamliel C Sevignani M Ferracin CD Dumitru M Shimizu S Zupo M Dono H Alder F Bullrich M Negrini CM Croce 2004 An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues Proc Natl Acad Sci USA 101 9740 9744 10.1073/pnas.0403293101 15210942 (Pubitemid 38869306)
35. CS Lobsiger DW Cleveland 2007 Glial cells as intrinsic components of non-cell-autonomous neurodegenerative disease Nat Neurosci 10 1355 1360 10.1038/nn1988 17965655 (Pubitemid 350014678)
36. G Lugli VI Torvik J Larson NR Smalheiser 2008 Expression of microRNAs and their precursors in synaptic fractions of adult mouse forebrain J Neurochem 106 650 661 10.1111/j.1471-4159.2008.05413.x 18410515
37. WJ Lukiw Y Zhao JG Cui 2008 An NF-kappaB-sensitive micro RNA-146a-mediated inflammatory circuit in Alzheimer disease and in stressed human brain cells J Biol Chem 283 31315 31322 10.1074/jbc.M805371200 18801740
38. PA Maroney S Chamnongpol F Souret TW Nilsen 2007 A rapid, quantitative assay for direct detection of microRNAs and other small RNAs using splinted ligation RNA 13 930 936 10.1261/rna.518107 17456563 (Pubitemid 46799827)
39. E Masliah ES Roberts D Langford I Everall L Crews A Adame E Rockenstein HS Fox 2004 Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis J Neuroimmunol 157 163 175 10.1016/j.jneuroim.2004.08.026 15579294 (Pubitemid 39576651)
40. Nelson PT, Wilfred BR (2009) In situ hybridization is a necessary experimental complement to microRNA (miRNA) expression profiling in the human brain. Neurosci Lett
41. TW Nilsen 2007 Mechanisms of microRNA-mediated gene regulation in animal cells Trends Genet 23 243 249 10.1016/j.tig.2007.02.011 17368621 (Pubitemid 46628981)
42. GJ Nuovo 2008 In situ detection of precursor and mature microRNAs in paraffin embedded, formalin fixed tissues and cell preparations Methods 44 39 46 10.1016/j.ymeth.2007.10.008 18158131 (Pubitemid 350297988)
43. G Nuovo EJ Lee S Lawler J Godlewski T Schmittgen 2009 In situ detection of mature microRNAs by labeled extension on ultramer templates Biotechniques 46 115 126 10.2144/000113068 19317656
44. GJ Nuovo TS Elton P Nana-Sinkam S Volinia CM Croce TD Schmittgen 2009 A methodology for the combined in situ analyses of the precursor and mature forms of microRNAs and correlation with their putative targets Nat Protoc 4 107 115 10.1038/nprot.2008.215 19131963
45. AN Packer Y Xing SQ Harper L Jones BL Davidson 2008 The bifunctional microRNA miR-9/miR-9regulates REST and CoREST and is downregulated in Huntington's disease J Neurosci 28 14341 14346 10.1523/JNEUROSCI.2390-08.2008 19118166
46. JC Pang WK Kwok Z Chen HK Ng 2009 Oncogenic role of microRNAs in brain tumors Acta neuropathologica 117 599 611 10.1007/s00401-009-0525-0 19343354
47. JT Pena C Sohn-Lee SH Rouhanifard J Ludwig M Hafner A Mihailovic C Lim D Holoch P Berninger M Zavolan T Tuschl 2009 miRNA in situ hybridization in formaldehyde and EDC-fixed tissues Nat Methods 6 139 141 10.1038/nmeth.1294 19137005
48. L Peters G Meister 2007 Argonaute proteins: mediators of RNA silencing Mol Cell 26 611 623 10.1016/j.molcel.2007.05.001 17560368 (Pubitemid 46856239)
49. RS Pillai 2005 MicroRNA function: multiple mechanisms for a tiny RNA? RNA 11 1753 1761 10.1261/rna.2248605 16314451 (Pubitemid 41720024)
50. R Rademakers, et al. 2008 Common variation in the miR-659 binding-site of GRN is a major risk factor for TDP43-positive frontotemporal dementia Hum Mol Genet 17 3631 3642 10.1093/hmg/ddn257 18723524
51. BJ Reinhart G Ruvkun 2001 Isoform-specific mutations in the Caenorhabditis elegans heterochronic gene lin-14 affect stage-specific patterning Genetics 157 199 209 11139502
52. BJ Reinhart FJ Slack M Basson AE Pasquinelli JC Bettinger AE Rougvie HR Horvitz G Ruvkun 2000 The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 901 906 10.1038/35002607 10706289 (Pubitemid 30130993)
53. I Rigoutsos 2009 New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites Cancer Res 69 3245 3248 10.1158/0008-5472.CAN-09-0352 19351814
54. ES Roberts MA Zandonatti DD Watry LJ Madden SJ Henriksen MA Taffe HS Fox 2003 Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS Am J Pathol 162 2041 2057 12759259
55. ES Roberts S Huitron-Resendiz MA Taffe MC Marcondes CT Flynn CM Lanigan JA Hammond SR Head SJ Henriksen HS Fox 2006 Host response and dysfunction in the CNS during chronic simian immunodeficiency virus infection J Neurosci 26 4577 4585 10.1523/JNEUROSCI.4504-05.2006 16641237 (Pubitemid 44315357)
56. R Saba CD Goodman RL Huzarewich C Robertson SA Booth 2008 A miRNA signature of prion induced neurodegeneration PLoS ONE 3 e3652 10.1371/journal.pone.0003652 18987751
57. JN Savas A Makusky S Ottosen D Baillat F Then D Krainc R Shiekhattar SP Markey N Tanese 2008 Huntington's disease protein contributes to RNA-mediated gene silencing through association with Argonaute and P bodies Proc Natl Acad Sci USA 105 10820 10825 10.1073/pnas.0800658105 18669659
58. GM Schratt F Tuebing EA Nigh CG Kane ME Sabatini M Kiebler ME Greenberg 2006 A brain-specific microRNA regulates dendritic spine development Nature 439 283 289 10.1038/nature04367 16421561 (Pubitemid 43128846)
59. EM Schuman JL Dynes O Steward 2006 Synaptic regulation of translation of dendritic mRNAs J Neurosci 26 7143 7146 10.1523/JNEUROSCI.1796-06.2006 16822969
60. M Selbach B Schwanhausser N Thierfelder Z Fang R Khanin N Rajewsky 2008 Widespread changes in protein synthesis induced by microRNAs Nature 455 58 63 10.1038/nature07228 18668040
61. P Sethi WJ Lukiw 2009 Micro-RNA abundance and stability in human brain: specific alterations in Alzheimer's disease temporal lobe neocortex Neurosci Lett 459 100 104 10.1016/j.neulet.2009.04.052 19406203
62. G Siegel, et al. 2009 A functional screen implicates microRNA-138- dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis Nat Cell Biol 11 705 716 10.1038/ncb1876 19465924
63. A Valoczi C Hornyik N Varga J Burgyan S Kauppinen Z Havelda 2004 Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes Nucleic Acids Res 32 e175 10.1093/nar/gnh171 15598818
64. N Vo ME Klein O Varlamova DM Keller T Yamamoto RH Goodman S Impey 2005 A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis Proc Natl Acad Sci USA 102 16426 16431 10.1073/pnas.0508448102 16260724 (Pubitemid 41688930)
65. WX Wang BW Rajeev AJ Stromberg N Ren G Tang Q Huang I Rigoutsos PT Nelson 2008 The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1 J Neurosci 28 1213 1223 10.1523/JNEUROSCI. 5065-07.2008 18234899 (Pubitemid 351186356)
66. E Wienholds MJ Koudijs FJ van Eeden E Cuppen RH Plasterk 2003 The microRNA-producing enzyme Dicer1 is essential for zebrafish development Nat Genet 35 217 218 10.1038/ng1251 14528306 (Pubitemid 37363173)