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RNA-binding protein research with transcriptome-wide technologies in neural development

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Abstract

An increasing number of studies have demonstrated that neural RNA-binding proteins (nRNABPs) participate in several steps of neural development through post-transcriptional regulation of their RNA targets (Grabowski Curr Opin Genet Dev 21:388–394, 2011). Classical genetics and in vitro biochemical approaches have identified several important RNA targets of nRNABPs linked to cell-fate decision and neuronal functions. In recent years, new technologies, such as unbiased in vivo protein–RNA interaction approaches, high-throughput sequencing-cross-linked immunoprecipitation (HITS-CLIP), microarrays, RNAseq and others, have been developed. The use of these with genetics has succeeded in defining a dynamic range of RNA targets of RNABPs at the transcriptome-wide level. This new platform also provides the mechanistic insights into a specific biological function of nRNABPs. This review highlights the discoveries and challenges of the interplay between the nRNABPs and their biological functions in neural development.

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References

  1. Akamatsu W, Okano HJ, Osumi N, Inoue T, Nakamura S, Sakakibara S, Miura M, Matsuo N, Darnell RB, Okano H (1999) Mammalian ELAV-like neuronal RNA-binding proteins HuB and HuC promote neuronal development in both the central and the peripheral nervous systems. Proc Natl Acad Sci USA 96:9885–9890

  2. Akamatsu W, Fujihara H, Mitsuhashi T, Yano M, Shibata S, Hayakawa Y, Okano HJ, Sakakibara S, Takano H, Takano T, Takahashi T, Noda T, Okano H (2005) The RNA-binding protein HuD regulates neuronal cell identity and maturation. Proc Natl Acad Sci USA 102:4625–4630

  3. Antic D, Lu N, Keene JD (1999) ELAV tumor antigen, Hel-N1, increases translation of neurofilament M mRNA and induces formation of neurites in human teratocarcinoma cells. Genes Dev 13:449–461

  4. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

  5. Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares MJ, Black DL (2007) A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21:1636–1652

  6. Buckanovich RJ, Darnell RB (1997) The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo. Mol Cell Biol 17:3194–3201

  7. Buckanovich RJ, Yang YY, Darnell RB (1996) The onconeural antigen Nova-1 is a neuron-specific RNA-binding protein, the activity of which is inhibited by paraneoplastic antibodies. J Neurosci 16:1114–1122

  8. Charizanis K, Lee KY, Batra R, Goodwin M, Zhang C, Yuan Y, Shiue L, Cline M, Scotti MM, Xia G, Kumar A, Ashizawa T, Clark HB, Kimura T, Takahashi MP, Fujimura H, Jinnai K, Yoshikawa H, Gomes-Pereira M, Gourdon G, Sakai N, Nishino S, Foster TC, Ares MJ, Darnell RB, Swanson MS (2012) Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy. Neuron 75:437–450

  9. Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460:479–486

  10. Chung S, Eckrich M, Perrone-Bizzozero N, Kohn DT, Furneaux H (1997) The Elav-like proteins bind to a conserved regulatory element in the 3’untranslated region of GAP-43 mRNA. J Biol Chem 272:6593–6598

  11. Cooper TA, Wan L, Dreyfuss G (2009) RNA and disease. Cell 136:777–793

  12. Darnell RB (2013) RNA protein interaction in neurons. Annu Rev Neurosci 36:243–270

  13. Darnell RB, Posner JB (2003) Paraneoplastic syndromes involving the nervous system. N Engl J Med 349:1543–1554

  14. Darnell JC, Van Driesche SJ, Zhang C, Hung KY, Mele A, Fraser CE, Stone EF, Chen C, Fak JJ, Chi SW, Licatalosi DD, Richter JD, Darnell RB (2011) FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 146:247–261

  15. Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, Ma G, Bupp S, Shrestha P, Shah RD, Doughty ML, Gong S, Greengard P, Heintz N (2008) Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135:749–762

  16. Gehman LT, Stoilov P, Maguire J, Damianov A, Lin CH, Shiue L, Ares MJ, Mody I, Black DL (2011) The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet 43:706–711

  17. Gehman LT, Meera P, Stoilov P, Shiue L, O’rien JE, Meisler MH, Ares MJ, Otis TS, Black DL (2012) The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes Dev 26:445–460

  18. Grabowski P (2011) Alternative splicing takes shape during neuronal development. Curr Opin Genet Dev 21:388–394

  19. Heiman M, Schaefer A, Gong S, Peterson JD, Day M, Ramsey KE, Suarez-Farinas M, Schwarz C, Stephan DA, Surmeier DJ, Greengard P, Heintz N (2008) A translational profiling approach for the molecular characterization of CNS cell types. Cell 135:738–748

  20. Helwak A, Kudla G, Dudnakova T, Tollervey D (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153:654–665

  21. Huang CS, Shi SH, Ule J, Ruggiu M, Barker LA, Darnell RB, Jan YN, Jan LY (2005) Common molecular pathways mediate long-term potentiation of synaptic excitation and slow synaptic inhibition. Cell 123:105–118

  22. Imai T, Tokunaga A, Yoshida T, Hashimoto M, Mikoshiba K, Weinmaster G, Nakafuku M, Okano H (2001) The neural RNA-binding protein Musashi1 translationally regulates mammalian numb gene expression by interacting with its mRNA. Mol Cell Biol 21:3888–3900

  23. Ince-Dunn G, Okano HJ, Jensen KB, Park WY, Zhong R, Ule J, Mele A, Fak JJ, Yang C, Zhang C, Yoo J, Herre M, Okano H, Noebels JL, Darnell RB (2012) Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability. Neuron 75:1067–1080

  24. Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15:205–213

  25. Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802

  26. Jensen KB, Dredge BK, Stefani G, Zhong R, Buckanovich RJ, Okano HJ, Yang YY, Darnell RB (2000) Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron 25:359–371

  27. Jin Y, Suzuki H, Maegawa S, Endo H, Sugano S, Hashimoto K, YasudaK, Inoue K (2003). A vertebrate RNA-binding protein Fox-1 regulatestissue-specific splicing via the pentanucleotide GCAUG. EMBO J 22:905–912

  28. Joseph B, Orlian M, Furneaux H (1998) p21(waf1) mRNA contains a conserved element in its 3’untranslated region that is bound by the Elav-like mRNA-stabilizing proteins. J Biol Chem 273:20511–20516

  29. Kawahara H, Imai T, Imataka H, Tsujimoto M, Matsumoto K, Okano H (2008) Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP. J Cell Biol 181:639–653

  30. Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17:909–915

  31. Konig J, Zarnack K, Luscombe NM, Ule J (2011) Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 13:77–83

  32. Li Q, Zheng S, Han A, Lin CH, Stoilov P, Fu XD, Black DL (2014) The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. Elife 3:e01201

  33. Licatalosi DD, Darnell RB (2010) RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11:75–87

  34. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456:464–469

  35. Licatalosi DD, Yano M, Fak JJ, Mele A, Grabinski SE, Zhang C, Darnell RB (2012) Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev 26:1626–1642

  36. Lisbin MJ, Qiu J, White K (2001) The neuron-specific RNA-binding protein ELAV regulates neuroglian alternative splicing in neurons and binds directly to its pre-mRNA. Genes Dev 15:2546–2561

  37. Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY (2012) Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol Cell 48:760–770

  38. Makeyev EV, Zhang J, Carrasco MA, Maniatis T (2007) The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell 27:435–448

  39. Martin CL, Duvall JA, Ilkin Y, Simon JS, Arreaza MG, Wilkes K, Alvarez-Retuerto A, Whichello A, Powell CM, Rao K, Cook E, Geschwind DH (2007) Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am J Med Genet B 144B:869–876

  40. Nakamura M, Okano H, Blendy JA, Montell C (1994) Musashi, a neural RNA-binding protein required for Drosophila adult external sensory organ development. Neuron 13:67–81

  41. Okabe M, Imai T, Kurusu M, Hiromi Y, Okano H (2001) Translational repression determines a neuronal potential in Drosophila asymmetric cell division. Nature 411:94–98

  42. Polydorides AD, Okano HJ, Yang YY, Stefani G, Darnell RB (2000) A brain-enriched polypyrimidine tract-binding protein antagonizes the ability of Nova to regulate neuron-specific alternative splicing. Proc Natl Acad Sci USA 97:6350–6355

  43. Richter JD, Treisman JE (2011) Not just the messenger: RNA takes control. Curr Opin Genet Dev 21:363–365

  44. Robinow S, Campos AR, Yao KM, White K (1988) The elav gene product of Drosophila, required in neurons, has three RNP consensus motifs. Science 242:1570–1572

  45. Ruggiu M, Herbst R, Kim N, Jevsek M, Fak JJ, Mann MA, Fischbach G, Burden SJ, Darnell RB (2009) Rescuing Z + agrin splicing in Nova null mice restores synapse formation and unmasks a physiologic defect in motor neuron firing. Proc Natl Acad Sci USA 106:3513–3518

  46. Saffary R, Xie Z (2011) FMRP regulates the transition from radial glial cells to intermediate progenitor cells during neocortical development. J Neurosci 31:1427–1439

  47. Sakakibara S, Imai T, Hamaguchi K, Okabe M, Aruga J, Nakajima K, Yasutomi D, Nagata T, Kurihara Y, Uesugi S, Miyata T, Ogawa M, Mikoshiba K, Okano H (1996) Mouse-Musashi-1, a neural RNA-binding protein highly enriched in the mammalian CNS stem cell. Dev Biol 176:230–242

  48. Sakakibara S, Nakamura Y, Satoh H, Okano H (2001) Rna-binding protein Musashi2: developmentally regulated expression in neural precursor cells and subpopulations of neurons in mammalian CNS. J Neurosci 21:8091–8107

  49. Sakakibara S, Nakamura Y, Yoshida T, Shibata S, Koike M, Takano H, Ueda S, Uchiyama Y, Noda T, Okano H (2002) RNA-binding protein Musashi family: roles for CNS stem cells and a subpopulation of ependymal cells revealed by targeted disruption and antisense ablation. Proc Natl Acad Sci USA 99:15194–15199

  50. Shibasaki T, Tokunaga A, Sakamoto R, Sagara H, Noguchi S, Sasaoka T, Yoshida N (2013) PTB deficiency causes the loss of adherens junctions in the dorsal telencephalon and leads to lethal hydrocephalus. Cereb Cortex 23:1824–1835

  51. Soller M, White K (2003) ELAV inhibits 3’end processing to promote neural splicing of ewg pre-mRNA. Genes Dev 17:2526–2538

  52. Szabo A, Dalmau J, Manley G, Rosenfeld M, Wong E, Henson J, Posner JB, Furneaux HM (1991) HuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding domains and is homologous to Elav and Sex-lethal. Cell 67:325–333

  53. Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, Konig J, Hortobagyi T, Nishimura AL, Zupunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE, Ule J (2011) Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci 14:452–458

  54. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, Blencowe BJ, Prasanth SG, Prasanth KV (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925–938

  55. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302:1212–1215

  56. Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB (2005) Nova regulates brain-specific splicing to shape the synapse. Nat Genet 37:844–852

  57. Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lecuyer E, Burge CB (2012) Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150:710–724

  58. Xue Y, Zhou Y, Wu T, Zhu T, Ji X, Kwon YS, Zhang C, Yeo G, Black DL, Sun H, Fu XD, Zhang Y (2009) Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell 36:996–1006

  59. Yano M, Okano HJ, Okano H (2005) Involvement of Hu and heterogeneous nuclear ribonucleoprotein K in neuronal differentiation through p21 mRNA post-transcriptional regulation. J Biol Chem 280:12690–12699

  60. Yano M, Hayakawa-Yano Y, Mele A, Darnell RB (2010) Nova2 regulates neuronal migration through an RNA switch in disabled-1 signaling. Neuron 66:848–858

  61. Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH (2009) An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 16:130–137

  62. Zhang C, Darnell RB (2011) Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 29:607–614

  63. Zhang YQ, Bailey AM, Matthies HJ, Renden RB, Smith MA, Speese SD, Rubin GM, Broadie K (2001) Drosophila fragile X-related gene regulates the MAP1B homolog Futsch to control synaptic structure and function. Cell 107:591–603

  64. Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB, Wang H, Licatalosi DD, Fak JJ, Darnell RB (2010) Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science 329:439–443

  65. Zheng S, Gray EE, Chawla G, Porse BT, O’ell TJ, Black DL (2012) PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat Neurosci 15(381–8):S1

  66. Zhong XY, Wang P, Han J, Rosenfeld MG, Fu XD (2009) SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol Cell 35:1–10

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Acknowledgments

The authors would like to thank Dr. Yoshika Yano for a critical reading. This work was supported by “Funding Program for World-leading Innovative R&D on Science and Technology” to H.O. and the MEXT Grant-in-Aid for Young Scientists, the Takeda Science Foundation for medical science research, Keio Gijuku Academic Development Funds and the Mochida Memorial Foundation for medical and pharmaceutical research to M.Y.

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Correspondence to Masato Yano or Hideyuki Okano.

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Yano, M., Ohtsuka, T. & Okano, H. RNA-binding protein research with transcriptome-wide technologies in neural development. Cell Tissue Res 359, 135–144 (2015). https://doi.org/10.1007/s00441-014-1923-8

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Keywords

  • RNA-binding protein
  • HITS-CLIP
  • Neural development