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PMID: 27669990 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Evolving insights into RNA modifications and their functional diversity in the brain.

Nature neuroscience ·Vol. 19 ·No. 10 ·2016-00-27 ·Pages 1292-8

Nainar S, Marshall PR, Tyler CR, Spitale RC, Bredy TW

Abstract

In this Perspective, we expand the notion of temporal regulation of RNA in the brain and propose that the qualitative nature of RNA and its metabolism, together with RNA abundance, are essential for the molecular mechanisms underlying experience-dependent plasticity. We discuss emerging concepts in the newly burgeoning field of epitranscriptomics, which are predicted to be heavily involved in cognitive function. These include activity-induced RNA modifications, RNA editing, dynamic changes in the secondary structure of RNA, and RNA localization. Each is described with an emphasis on its role in regulating the function of both protein-coding genes, as well as various noncoding regulatory RNAs, and how each might influence learning and memory.

MeSH Terms
Animals Brain/metabolism Cognition Humans Learning Neurons/metabolism RNA/metabolism RNA, Untranslated/metabolism
Chemicals
RNA, Untranslated RNA
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Nainar Sarah
Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA.
Marshall Paul R
Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA. | Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA.
Tyler Christina R
Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA. | Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA.
Spitale Robert C
Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA.
Bredy Timothy W
Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA. | Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA. | Queensland Brain Institute, University of Queensland, Brisbane, Australia.
References (84)
84 references, click to expand
  1. Ribosomal RNA pseudouridines and pseudouridine synthases.
    FEBS Lett. 2002 Mar 6;514(1):17-25 PMID: 11904174
  2. Real-time quantification of single RNA translation dynamics in living cells.
    Science. 2016 Jun 17;352(6292):1425-9 PMID: 27313040
  3. N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency.
    Cell. 2015 Jun 4;161(6):1388-99 PMID: 26046440
  4. Molecular identification of pseudouridine-metabolizing enzymes.
    J Biol Chem. 2008 Sep 12;283(37):25238-46 PMID: 18591240
  5. Patterns of developmental expression of the RNA editing enzyme rADAR2.
    Neuroscience. 2000;95(3):869-79 PMID: 10670454
  6. Memory--a century of consolidation.
    Science. 2000 Jan 14;287(5451):248-51 PMID: 10634773
  7. The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry.
    Nat Neurosci. 2013 Aug;16(8):1042-8 PMID: 23817550
  8. Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
    Cell. 2016 Apr 7;165(2):488-96 PMID: 26997482
  9. Dynamic DNA methylation: a prime candidate for genomic metaplasticity and behavioral adaptation.
    Trends Neurosci. 2013 Jan;36(1):3-13 PMID: 23041052
  10. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.
    Mol Syst Biol. 2014 Dec 23;10:770 PMID: 25538139
  11. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.
    Nature. 2014 Jan 30;505(7485):701-5 PMID: 24336214
  12. Transglycosylation: a mechanism for RNA modification (and editing?).
    Bioorg Chem. 2005 Jun;33(3):229-51 PMID: 15888313
  13. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.
    Cell. 2012 Jun 22;149(7):1635-46 PMID: 22608085
  14. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression.
    EMBO J. 2010 Sep 15;29(18):3082-93 PMID: 20729808
  15. Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated With Anxiety-like Behavior in Mice.
    Biol Psychiatry. 2015 Dec 15;78(12 ):848-59 PMID: 25792222
  16. APEX Fingerprinting Reveals the Subcellular Localization of Proteins of Interest.
    Cell Rep. 2016 May 24;15(8):1837-47 PMID: 27184847
  17. RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5' splice site.
    Mol Cell Biol. 2011 May;31(9):1812-21 PMID: 21343338
  18. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.
    Science. 2016 Jun 24;352(6293):1586-90 PMID: 27339989
  19. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.
    Mol Cell. 2014 Jul 17;55(2):332-41 PMID: 25002142
  20. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses.
    Nat Rev Genet. 2012 Mar 13;13(4):227-32 PMID: 22411467
  21. RNA modifications: what have we learned and where are we headed?
    Nat Rev Genet. 2016 Jun;17 (6):365-72 PMID: 27140282
  22. RNA-guided isomerization of uridine to pseudouridine--pseudouridylation.
    RNA Biol. 2014;11(12):1483-94 PMID: 25590339
  23. Formation of the conserved pseudouridine at position 55 in archaeal tRNA.
    Nucleic Acids Res. 2006;34(15):4293-301 PMID: 16920741
  24. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements.
    Nature. 2011 Feb 10;470(7333):284-8 PMID: 21307942
  25. Comparative conformations of uridine and pseudouridine and their derivatives.
    Eur J Biochem. 1980 Jul;108(2):457-63 PMID: 7408861
  26. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.
    Genome Res. 2014 Mar;24(3):365-76 PMID: 24347612
  27. Deciphering the functions and regulation of brain-enriched A-to-I RNA editing.
    Nat Neurosci. 2013 Nov;16(11):1518-22 PMID: 24165678
  28. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome.
    Nat Chem Biol. 2015 Aug;11(8):592-7 PMID: 26075521
  29. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.
    Cell Rep. 2012 Jul 26;2(1):111-23 PMID: 22840402
  30. Genome-wide translational profiling by ribosome footprinting.
    Methods Enzymol. 2010;470:119-42 PMID: 20946809
  31. Insights into RNA structure and function from genome-wide studies.
    Nat Rev Genet. 2014 Jul;15(7):469-79 PMID: 24821474
  32. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.
    Science. 2016 Aug 5;353(6299):aaf5573 PMID: 27256883
  33. The birth of the Epitranscriptome: deciphering the function of RNA modifications.
    Genome Biol. 2012 Oct 31;13(10):175 PMID: 23113984
  34. RNA epigenetics--chemical messages for posttranscriptional gene regulation.
    Curr Opin Chem Biol. 2016 Feb;30:46-51 PMID: 26625014
  35. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions.
    Nature. 2015 Feb 26;518(7540):560-4 PMID: 25719671
  36. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses.
    RNA. 2004 Nov;10(11):1692-4 PMID: 15388877
  37. MODOMICS: a database of RNA modification pathways--2013 update.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D262-7 PMID: 23118484
  38. Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage.
    RNA. 2013 Feb;19(2):257-70 PMID: 23264566
  39. Understanding the transcriptome through RNA structure.
    Nat Rev Genet. 2011 Aug 18;12(9):641-55 PMID: 21850044
  40. Dynamic m(6)A mRNA methylation directs translational control of heat shock response.
    Nature. 2015 Oct 22;526(7574):591-4 PMID: 26458103
  41. Neural plasticity and behavior - sixty years of conceptual advances.
    J Neurochem. 2016 Oct;139 Suppl 2:179-199 PMID: 26875778
  42. CLIP: a method for identifying protein-RNA interaction sites in living cells.
    Methods. 2005 Dec;37(4):376-86 PMID: 16314267
  43. Global quantification of mammalian gene expression control.
    Nature. 2011 May 19;473(7347):337-42 PMID: 21593866
  44. Pseudouridine in mRNA: Incorporation, Detection, and Recoding.
    Methods Enzymol. 2015;560:187-217 PMID: 26253972
  45. Modulation of RNA editing by functional nucleolar sequestration of ADAR2.
    Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14018-23 PMID: 14612560
  46. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
    Nature. 2012 Apr 29;485(7397):201-6 PMID: 22575960
  47. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.
    Nat Biotechnol. 2011 May;29(5):436-42 PMID: 21516085
  48. Can changes in histone acetylation contribute to memory formation?
    Trends Genet. 2014 Dec;30(12):529-39 PMID: 25269450
  49. Accurate identification of human Alu and non-Alu RNA editing sites.
    Nat Methods. 2012 Jun;9(6):579-81 PMID: 22484847
  50. Modulation of ADAR1 editing activity by Z-RNA in vitro.
    Nucleic Acids Res. 2005 Sep 21;33(16):5362-70 PMID: 16177183
  51. N6-methyladenosine marks primary microRNAs for processing.
    Nature. 2015 Mar 26;519(7544):482-5 PMID: 25799998
  52. RNA Editing: A Contributor to Neuronal Dynamics in the Mammalian Brain.
    Trends Genet. 2016 Mar;32(3):165-75 PMID: 26803450
  53. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA.
    Nature. 2016 Feb 25;530(7591):441-6 PMID: 26863196
  54. The role of regulatory RNA in cognitive evolution.
    Trends Cogn Sci. 2012 Oct;16(10):497-503 PMID: 22940578
  55. MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise.
    Nat Commun. 2013;4:2364 PMID: 24077216
  56. System wide analyses have underestimated protein abundances and the importance of transcription in mammals.
    PeerJ. 2014 Feb 27;2:e270 PMID: 24688849
  57. Progress and challenges for chemical probing of RNA structure inside living cells.
    Nat Chem Biol. 2015 Dec;11(12):933-41 PMID: 26575240
  58. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT.
    Science. 2005 Sep 2;309(5740):1570-3 PMID: 16141075
  59. Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling.
    Science. 2014 Nov 7;346(6210):1257521 PMID: 25378630
  60. Involvement of the 3'-untranslated region of the brain-derived neurotrophic factor gene in activity-dependent mRNA stabilization.
    J Neurochem. 2010 Dec;115(5):1222-33 PMID: 20874756
  61. The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing.
    Mol Psychiatry. 2014 Apr;19(4):486-94 PMID: 23628989
  62. Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
    Mol Syst Biol. 2016 Jan 20;12 (1):855 PMID: 26792871
  63. Structural and functional characterization of the proteins responsible for N6-methyladenosine modification and recognition.
    Curr Protein Pept Sci. 2015 Jun 22;:null PMID: 26100282
  64. Widespread RNA editing of embedded alu elements in the human transcriptome.
    Genome Res. 2004 Sep;14(9):1719-25 PMID: 15342557
  65. N6-methyladenosine–encoded epitranscriptomics.
    Nat Struct Mol Biol. 2016 Feb;23(2):98-102 PMID: 26840897
  66. Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling.
    Science. 2014 Nov 7;346(6210):748-51 PMID: 25378625
  67. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.
    Science. 2015 Mar 6;347(6226):1259038 PMID: 25745177
  68. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells.
    Nature. 2014 Nov 6;515(7525):143-6 PMID: 25192136
  69. The dynamic epitranscriptome: N6-methyladenosine and gene expression control.
    Nat Rev Mol Cell Biol. 2014 May;15(5):313-26 PMID: 24713629
  70. Association of Argonaute proteins and microRNAs can occur after cell lysis.
    RNA. 2012 Sep;18(9):1581-5 PMID: 22836356
  71. Pseudouridine in RNA: what, where, how, and why.
    IUBMB Life. 2000 May;49(5):341-51 PMID: 10902565
  72. Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure.
    Biochemistry. 1994 Jun 21;33(24):7560-7 PMID: 8011621
  73. Stabilization of RNA stacking by pseudouridine.
    Nucleic Acids Res. 1995 Dec 25;23(24):5020-6 PMID: 8559660
  74. G-quadruplex RNA structure as a signal for neurite mRNA targeting.
    EMBO Rep. 2011 Jul 01;12(7):697-704 PMID: 21566646
  75. Mechanisms of RNA localization and translational regulation.
    Curr Opin Genet Dev. 2000 Oct;10(5):476-88 PMID: 10980424
  76. RNA pseudouridylation: new insights into an old modification.
    Trends Biochem Sci. 2013 Apr;38(4):210-8 PMID: 23391857
  77. The regulation of transcription in memory consolidation.
    Cold Spring Harb Perspect Biol. 2014 Dec 04;7(1):a021741 PMID: 25475090
  78. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation.
    Nat Rev Mol Cell Biol. 2016 Jan;17(1):5-15 PMID: 26670017
  79. Gene expression regulation mediated through reversible m⁶A RNA methylation.
    Nat Rev Genet. 2014 May;15(5):293-306 PMID: 24662220
  80. Post-transcriptional nucleotide modification and alternative folding of RNA.
    Nucleic Acids Res. 2006 Feb 01;34(2):721-33 PMID: 16452298
  81. Processive DNA demethylation via DNA deaminase-induced lesion resolution.
    PLoS One. 2014 Jul 15;9(7):e97754 PMID: 25025377
  82. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.
    Nature. 2014 Jan 30;505(7485):696-700 PMID: 24270811
  83. Structural imprints in vivo decode RNA regulatory mechanisms.
    Nature. 2015 Mar 26;519(7544):486-90 PMID: 25799993
  84. Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice.
    J Neurosci. 2016 Jun 22;36(25):6771-7 PMID: 27335407
Article Info
Journal
Nature neuroscience
Abbr.
Nat Neurosci
ISSN
1546-1726
Published
2016-00-27
Pages
1292-8
Language
English
Region
United States
NLM ID
9809671
PMCID
PMC5068363
Subset
IM
Grants
NIGMS NIH HHS · DP2 GM119164 · United States
NIMH NIH HHS · R01 MH105398 · United States
NIMH NIH HHS · R01 MH109588 · United States
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