Non-coding RNA networks underlying cognitive disorders across the lifespan

Trends in Molecular Medicine

Volumn 17, Issue 6, 2011, Pages 337-346

  Qureshi, Irfan A ^a   Mehler, Mark F ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

AGING; BRAIN DEVELOPMENT; CENTRAL NERVOUS SYSTEM; COGNITIVE DEFECT; EPIGENETICS; GENE FUNCTION; GENOME IMPRINTING; HUMAN; LIFESPAN; NERVE CELL PLASTICITY; NONHUMAN; REVIEW; RNA EDITING; STRESS; X CHROMOSOME INACTIVATION;

AGING; BRAIN; COGNITION DISORDERS; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; MODELS, BIOLOGICAL; NERVOUS SYSTEM DISEASES; RNA, UNTRANSLATED;

EID: 79958770713     PISSN: 14714914     EISSN: 1471499X     Source Type: Journal    
DOI: 10.1016/j.molmed.2011.02.002     Document Type: Review

References (124)

1. Mehler M.F., Mattick J.S. Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol. Rev. 2007, 87:799-823.
2. Mehler M.F. Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog. Neurobiol. 2008, 86:305-341.
3. Mattick J.S., Mehler M.F. RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci. 2008, 31:227-233.
4. Mercer T.R., et al. Noncoding RNAs in long-term memory formation. Neuroscientist 2008, 14:434-445.
5. Majer A., Booth S.A. Computational methodologies for studying non-coding RNAs relevant to central nervous system function and dysfunction. Brain Res. 2010, 1338:131-145.
6. Yang J.H., et al. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010, 38:D123-D130.
7. Mercer T.R., et al. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:716-721.
8. Ponjavic J., et al. Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet. 2009, 5:e1000617.
9. Mercer T.R., et al. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci. 2010, 11:14.
10. Lau P., et al. Identification of dynamically regulated microRNA and mRNA networks in developing oligodendrocytes. J. Neurosci. 2008, 28:11720-11730.
11. Park C.S., Tang S.J. Regulation of microRNA expression by induction of bidirectional synaptic plasticity. J. Mol. Neurosci. 2009, 38:50-56.
12. Natera-Naranjo O., et al. Identification and quantitative analyses of microRNAs located in the distal axons of sympathetic neurons. RNA 2010, 16:1516-1529.
13. Dinger M.E., et al. RNAs as extracellular signaling molecules. J. Mol. Endocrinol. 2008, 40:151-159.
14. Mattick J.S., et al. RNA regulation of epigenetic processes. Bioessays 2009, 31:51-59.
15. Franklin T.B., Mansuy I.M. The prevalence of epigenetic mechanisms in the regulation of cognitive functions and behaviour. Curr. Opin. Neurobiol. 2010, 20:441-449.
16. Heimberg A.M., et al. MicroRNAs and the advent of vertebrate morphological complexity. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:2946-2950.
17. Taft R.J., et al. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007, 29:288-299.
18. Haygood R., et al. Contrasts between adaptive coding and noncoding changes during human evolution. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:7853-7857.
19. Pollard K.S., et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006, 443:167-172.
20. Tamura Y., et al. Epigenetic aberration of the human REELIN gene in psychiatric disorders. Mol. Psychiatry 2007, 12:519. 593-600.
21. Krol J., et al. The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet. 2010, 11:597-610.
22. Okamura K., Lai E.C. Endogenous small interfering RNAs in animals. Nat. Rev. Mol. Cell Biol. 2008, 9:673-678.
23. Coufal N.G., et al. L1 retrotransposition in human neural progenitor cells. Nature 2009, 460:1127-1131.
24. Muotri A.R., et al. L1 retrotransposition in neurons is modulated by MeCP2. Nature 2010, 468:443-446.
25. Zhou R., et al. Comparative analysis of argonaute-dependent small RNA pathways in Drosophila. Mol. Cell 2008, 32:592-599.
26. Verdel A., et al. Common themes in siRNA-mediated epigenetic silencing pathways. Int. J. Dev. Biol. 2009, 53:245-257.
27. Kishore S., Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 2006, 311:230-232.
28. Qureshi I.A., et al. Long non-coding RNAs in nervous system function and disease. Brain Res. 2010, 1338:20-35.
29. Orom U.A., et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010, 143:46-58.
30. Kapranov P., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488.
31. Birney E., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
32. Carninci P., et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
33. Katayama S., et al. Antisense transcription in the mammalian transcriptome. Science 2005, 309:1564-1566.
34. Taft R.J., et al. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat. Struct. Mol. Biol. 2010, 17:1030-1034.
35. Taft R.J., et al. Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle 2009, 8:2332-2338.
36. Belostotsky D. Exosome complex and pervasive transcription in eukaryotic genomes. Curr. Opin. Cell Biol. 2009, 21:352-358.
37. Kim T.K., et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010, 465:182-187.
38. Kapranov P., et al. New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature 2010, 466:642-646.
39. Taft R.J., et al. Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 2009, 41:572-578.
40. Taft R.J., et al. Small RNAs derived from snoRNAs. RNA 2009, 15:1233-1240.
41. Emara M.M., et al. Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J. Biol. Chem. 2010, 285:10959-10968.
42. Alliegro M.C., Alliegro M.A. Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:6993-6997.
43. Cao F., et al. Dicer independent small RNAs associate with telomeric heterochromatin. RNA 2009, 15:1274-1281.
44. Cui P., et al. A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 2010, 96:259-265.
45. Kapranov P., et al. The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol. 2010, 8:149.
46. van Bakel H., et al. Most " dark matter" transcripts are associated with known genes. PLoS Biol. 2010, 8:e1000371.
47. Marti E., et al. A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing. Nucleic Acids Res. 2010, 38:7219-7235.
48. St Laurent G., et al. Enhancing non-coding RNA information content with ADAR editing. Neurosci. Lett. 2009, 466:89-98.
49. Jacobs M.M., et al. ADAR1 and ADAR2 expression and editing activity during forebrain development. Dev. Neurosci. 2009, 31:223-237.
50. Melcher T., et al. RED2, a brain-specific member of the RNA-specific adenosine deaminase family. J. Biol. Chem. 1996, 271:31795-31798.
51. Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu. Rev. Biochem. 2010, 79:321-349.
52. Li J.B., et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 2009, 324:1210-1213.
53. Hundley H.A., Bass B.L. ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends Biochem. Sci. 2010, 35:377-383.
54. Kawahara Y., et al. Frequency and fate of microRNA editing in human brain. Nucleic Acids Res. 2008, 36:5270-5280.
55. Nicholas A., et al. Age-related gene-specific changes of A-to-I mRNA editing in the human brain. Mech. Ageing Dev. 2010, 131:445-447.
56. Montano, M. and Long, K. RNA surveillance - an emerging role for RNA regulatory networks in aging. Ageing Res. Rev. , (in press). doi:10.1016/j.arr.2010.02.002.
57. Sebastiani P., et al. RNA editing genes associated with extreme old age in humans and with lifespan in C. elegans. PLoS ONE 2009, 4:e8210.
58. Wang Y.J., et al. Expression and regulation of antiviral protein APOBEC3G in human neuronal cells. J. Neuroimmunol. 2009, 206:14-21.
59. Conticello S.G. The AID/APOBEC family of nucleic acid mutators. Genome Biol. 2008, 9:229.
60. Xing J., et al. Mobile DNA elements in primate and human evolution. Am. J. Phys. Anthropol. 2007, 45(Suppl.):2-19.
61. Britten R.J. Transposable element insertions have strongly affected human evolution. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:19945-19948.
62. Vuppalanchi D., et al. Regulation of mRNA transport and translation in axons. Results Probl. Cell Differ. 2009, 48:193-224.
63. Schratt G. microRNAs at the synapse. Nat. Rev. Neurosci. 2009, 10:842-849.
64. Bramham C.R. Local protein synthesis, actin dynamics, and LTP consolidation. Curr. Opin. Neurobiol. 2008, 18:524-531.
65. Cheever A., Ceman S. Translation regulation of mRNAs by the fragile X family of proteins through the microRNA pathway. RNA Biol. 2009, 6:175-178.
66. Li X., Jin P. Macro role(s) of microRNAs in fragile X syndrome?. Neuromol. Med. 2009, 11:200-207.
67. Anderson P., Kedersha N. RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat. Rev. Mol. Cell Biol. 2009, 10:430-436.
68. Mockett B.G., Hulme S.R. Metaplasticity: new insights through electrophysiological investigations. J. Integr. Neurosci. 2008, 7:315-336.
69. Willingham A.T., et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005, 309:1570-1573.
70. Arron J.R., et al. NFAT dysregulation by increased dosage of DSCR1 and DYRK1A on chromosome 21. Nature 2006, 441:595-600.
71. Abdul H.M., et al. Cognitive decline in Alzheimer's disease is associated with selective changes in calcineurin/NFAT signaling. J. Neurosci. 2009, 29:12957-12969.
72. Benner S.A. Extracellular 'communicator RNA'. FEBS Lett. 1988, 233:225-228.
73. Katakowski M., et al. Functional microRNA is transferred between glioma cells. Cancer Res. 2010, 70:8259-8263.
74. Smalheiser N.R. Exosomal transfer of proteins and RNAs at synapses in the nervous system. Biol. Direct 2007, 2:35.
75. Chen C., et al. Microfluidic isolation and transcriptome analysis of serum microvesicles. Lab. Chip 2010, 10:505-511.
76. Skog J., et al. Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat. Cell Biol. 2008, 10:1470-1476.
77. Feinberg E.H., Hunter C.P. Transport of dsRNA into cells by the transmembrane protein SID-1. Science 2003, 301:1545-1547.
78. Duxbury M.S., et al. RNA interference: a mammalian SID-1 homologue enhances siRNA uptake and gene silencing efficacy in human cells. Biochem. Biophys. Res. Commun. 2005, 331:459-463.
79. Lee J.T. The X as model for RNA's niche in epigenomic regulation. Cold Spring Harb. Perspect. Biol. 2010, 2:a003749.
80. Gecz J., et al. The genetic landscape of intellectual disability arising from chromosome X. Trends Genet. 2009, 25:308-316.
81. van Bokhoven H., Kramer J.M. Disruption of the epigenetic code: an emerging mechanism in mental retardation. Neurobiol. Dis. 2010, 39:3-12.
82. Bartolomei M.S. Genomic imprinting: employing and avoiding epigenetic processes. Genes Dev. 2009, 23:2124-2133.
83. Davies W., et al. Imprinted gene expression in the brain. Neurosci. Biobehav. Rev. 2005, 29:421-430.
84. Gregg C., et al. Sex-specific parent-of-origin allelic expression in the mouse brain. Science 2010, 329:682-685.
85. Gregg C., et al. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 2010, 329:643-648.
86. Davies W., et al. What are imprinted genes doing in the brain? Adv. Exp. Med. Biol. 2008, 626:62-70.
87. Cunningham M.D., et al. Chromatin modifiers, cognitive disorders, and imprinted genes. Dev. Cell 2010, 18:169-170.
88. Sahoo T., et al. Prader-Willi phenotype caused by paternal deficiency for the HBII-85C/D box small nucleolar RNA cluster. Nat. Genet. 2008, 40:719-721.
89. Lau P., Hudson L.D. MicroRNAs in neural cell differentiation. Brain Res. 2010, 1338:14-19.
90. Aimone J.B., et al. Adult neurogenesis: integrating theories and separating functions. Trends Cogn. Sci. 2010, 14:325-337.
91. Qureshi I.A., et al. REST and CoREST are transcriptional and epigenetic regulators of seminal neural fate decisions. Cell Cycle 2010, 9:4477-4486.
92. Kuwabara T., et al. The NRSE smRNA specifies the fate of adult hippocampal neural stem cells. Nucleic Acids Symp. Ser. (Oxf.) 2005, 49:87-88.
93. Lazarov O., et al. When neurogenesis encounters aging and disease. Trends Neurosci. 2010, 33:569-579.
94. Konopka W., et al. MicroRNA loss enhances learning and memory in mice. J. Neurosci. 2010, 30:14835-14842.
95. Wibrand K., et al. Differential regulation of mature and precursor microRNA expression by NMDA and metabotropic glutamate receptor activation during LTP in the adult dentate gyrus in vivo. Eur. J. Neurosci. 2010, 31:636-645.
96. Wu J., Xie X. Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression. Genome Biol. 2006, 7:R85.
97. Schratt G.M., et al. A brain-specific microRNA regulates dendritic spine development. Nature 2006, 439:283-289.
98. Gao J., et al. A novel pathway regulates memory and plasticity via SIRT1 and miR-134. Nature 2010, 466:1105-1109.
99. Vilardo E., et al. MicroRNA-101 regulates amyloid precursor protein expression in hippocampal neurons. J. Biol. Chem. 2010, 285:18344-18351.
100. Hebert S.S., et al. Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/beta-secretase expression. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:6415-6420.
101. Schonrock N., et al. Neuronal microRNA deregulation in response to Alzheimer's disease amyloid-beta. PLoS ONE 2010, 5:e11070.
102. Qureshi I.A., Mehler M.F. Regulation of non-coding RNA networks in the nervous system - what's the REST of the story?. Neurosci. Lett. 2009, 466:73-80.
103. Bond A.M., et al. Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat. Neurosci. 2009, 12:1020-1027.
104. Bernard D., et al. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010, 29:3082-3093.
105. Tripathi V., et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 2010, 39:925-938.
106. Lin D., et al. Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism. Mol. Cell Biol. 2008, 28:3008-3019.
107. Lewejohann L., et al. Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice. Behav. Brain Res. 2004, 154:273-289.
108. Mus E., et al. Dendritic BC200 RNA in aging and in Alzheimer's disease. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:10679-10684.
109. Massone S., et al. 17A, a novel non-coding RNA, regulates GABA B alternative splicing and signaling in response to inflammatory stimuli and in Alzheimer disease. Neurobiol. Dis. 2011, 41:308-317.
110. Faghihi M.A., et al. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 2008, 14:723-730.
111. Johnson, R. et al. The human accelerated region 1 noncoding RNA is repressed by REST in Huntington's disease. Physiol. Genomics, (in press). doi:10.1152/physiolgenomics.00019.2010.
112. Qureshi I.A., Mehler M.F. Epigenetic mechanisms underlying human epileptic disorders and the process of epileptogenesis. Neurobiol. Dis. 2010, 39:53-60.
113. Qureshi I.A., Mehler M.F. The emerging role of epigenetics in stroke: II. RNA regulatory circuitry. Arch. Neurol. 2010, 67:1435-1441.
114. Krechowec S., Plagge A. Physiological dysfunctions associated with mutations of the imprinted Gnas locus. Physiol. (Bethesda) 2008, 23:221-229.
115. Plagge A., et al. Imprinted Nesp55 influences behavioral reactivity to novel environments. Mol. Cell. Biol. 2005, 25:3019-3026.
116. Berridge C.W., Waterhouse B.D. The locus coeruleus-noradrenergic system: modulation of behavioral state and state-dependent cognitive processes. Brain Res. Brain Res. Rev. 2003, 42:33-84.
117. Burke S.N., Barnes C.A. Senescent synapses and hippocampal circuit dynamics. Trends Neurosci. 2010, 33:153-161.
118. Shamovsky I., et al. RNA-mediated response to heat shock in mammalian cells. Nature 2006, 440:556-560.
119. St Laurent G., Wahlestedt C. Noncoding RNAs: couplers of analog and digital information in nervous system function?. Trends Neurosci. 2007, 30:612-621.
120. Huarte M., et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142:409-419.
121. Wang X., et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008, 454:126-130.
122. Persengiev, S. et al. Genome-wide analysis of miRNA expression reveals a potential role for miR-144 in brain aging and spinocerebellar ataxia pathogenesis. Neurobiol. Aging, (in press). doi:10.1016/j.neurobiolaging.2010.03.014.
123. An J., et al. Identifying co-regulating microRNA groups. J. Bioinform. Comput. Biol. 2010, 8:99-115.
124. Nakamori M., Thornton C. Epigenetic changes and non-coding expanded repeats. Neurobiol. Dis. 2010, 39:21-27.