Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

RNA processing and its regulation: global insights into biological networks

Subjects

Key Points

  • The limited differences between the genomes of very different species have led to the emerging recognition that biological diversity is likely to largely derive from the complexity of RNA. This is evident in the diverse ways that RNA molecules are generated and processed and the various ways in which mRNA expression is regulated.

  • Just as new methodologies drove a revolution in our understanding of the role of RNA in biology in the twentieth century, new high-throughput sequencing, bioinformatics and biochemical methods are now being applied to whole tissues and genetically defined systems to generate new insights into the role of RNA in biological systems.

  • Alternative splicing is one of the best-studied mechanisms by which RNA diversity is generated. Regulation of splicing allows a means of generating RNA variants that offer great biological variability.

  • Alternative polyadenylation is emerging as an important means for regulating 3′ UTRs, which in turn offer various means of regulating gene expression, including microRNA-mediated control of translation, RNA localization and turnover.

  • The regulation of RNA processing involves a host of regulatory RNA-binding proteins (RNABPs) that act according to their affinities for different RNA sequences and the local abundances of RNAs and proteins. Therefore, a combination of biochemistry and cell biology will be required to fully understand RNA regulation in mammalian cells.

  • Genome-wide analysis of RNA–protein interactions can be rigorously approached biochemically using HITS-CLIP, and methods like next-generation sequencing offer a powerful means of quantifying RNA differences to enumerate RNA diversity. Putting the two approaches together using bioinformatic tools allows genome-wide functional RNA maps to be generated, and hence new rules of RNA regulation to be discovered.

  • An increasing number of human diseases are being found to relate to targeting of RNABPs, either through their mutation, autoimmune targeting or sequestration by RNA expansions. Applying these same genome-wide analyses to tissues affected by human disease offers the possibility of gaining new insights into disease pathogenesis and targeted therapeutics.

Abstract

In recent years views of eukaryotic gene expression have been transformed by the finding that enormous diversity can be generated at the RNA level. Advances in technologies for characterizing RNA populations are revealing increasingly complete descriptions of RNA regulation and complexity; for example, through alternative splicing, alternative polyadenylation and RNA editing. New biochemical strategies to map protein–RNA interactions in vivo are yielding transcriptome-wide insights into mechanisms of RNA processing. These advances, combined with bioinformatics and genetic validation, are leading to the generation of functional RNA maps that reveal the rules underlying RNA regulation and networks of biologically coherent transcripts. Together these are providing new insights into molecular cell biology and disease.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Alternative pre-mRNA processing allows a single gene to encode multiple mRNA isoforms.
Figure 2: Alternative splicing and polyadenylation.
Figure 3: Coupling of RNA processing to alternative RNA regulation.
Figure 4: Synergies between methods lead to new rules of RNA regulation.

References

  1. Sharp, P. A. The centrality of RNA. Cell 136, 577–580 (2009).

    Article  CAS  PubMed  Google Scholar 

  2. Scherrer, K., Latham, H. & Darnell, J. E. Demonstration of an unstable RNA and of a precursor to ribosomal RNA in HeLa cells. Proc. Natl Acad. Sci. USA 49, 240–248 (1963).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Soeiro, R., Vaughan, M. H., Warner, J. R. & Darnell, J. E. J. The turnover of nuclear DNA-like RNA in HeLa cells. J. Cell Biol. 39, 112–118 (1968).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Berk, A. J. & Sharp, P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12, 721–732 (1977).

    Article  CAS  PubMed  Google Scholar 

  5. Berget, S. M., Moore, C. & Sharp, P. A. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc. Natl Acad. Sci. USA 74, 3171–3175 (1977).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Chow, L. T., Gelinas, R. E., Broker, T. R. & Roberts, R. J. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12, 1–8 (1977).

    Article  CAS  PubMed  Google Scholar 

  7. Gilbert, W. Why genes in pieces? Nature 271, 501 (1978).

    Article  CAS  PubMed  Google Scholar 

  8. Breathnach, R., Mandel, J. L. & Chambon, P. Ovalbumin gene is split in chicken DNA. Nature 270, 314–319 (1977).

    Article  CAS  PubMed  Google Scholar 

  9. Tilghman, S. M. et al. Intervening sequence of DNA identified in the structural portion of a mouse β-globin gene. Proc. Natl Acad. Sci. USA 75, 725–729 (1978).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Crick, F. Split genes and RNA splicing. Science 204, 264–271 (1979).

    Article  CAS  PubMed  Google Scholar 

  11. Darnell, J. E. J. Implications of RNA–RNA splicing in evolution of eukaryotic cells. Science 202, 1257–1260 (1978).

    Article  CAS  PubMed  Google Scholar 

  12. Rogers, J. & Wall, R. Immunoglobulin RNA rearrangements in B lymphocyte differentiation. Adv. Immunol. 35, 39–59 (1984).

    Article  CAS  PubMed  Google Scholar 

  13. Amara, S. G., Jonas, V., Rosenfeld, M. G., Ong, E. S. & Evans, R. Alternative RNA processing in calcitonin gene expression generates mRNAs encoding different polypeptide products. Nature 298, 240–244 (1982).

    Article  CAS  PubMed  Google Scholar 

  14. Calarco, J. A. et al. Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev. 21, 2963–2975 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Cech, T. R. Crawling out of the RNA world. Cell 136, 599–602 (2009).

    Article  CAS  PubMed  Google Scholar 

  16. Zaug, A. J. & Cech, T. R. The intervening sequence RNA of Tetrahymena is an enzyme. Science 231, 470–475 (1986).

    Article  CAS  PubMed  Google Scholar 

  17. Carthew, R. W. & Sontheimer, E. J. Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642–655 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Malone, C. D. & Hannon, G. J. Small RNAs as guardians of the genome. Cell 136, 656–668 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mercer, T. R., Dinger, M. E. & Mattick, J. S. Long non-coding RNAs: insights into functions. Nature Rev. Genet. 10, 155–159 (2009).

    Article  CAS  PubMed  Google Scholar 

  20. Ponting, C. P., Oliver, P. L. & Reik, W. Evolution and functions of long noncoding RNAs. Cell 136, 629–641 (2009).

    Article  CAS  PubMed  Google Scholar 

  21. Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev. Genet. 9, 102–114 (2008).

    Article  CAS  PubMed  Google Scholar 

  22. Wang, X. et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454, 126–130 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Cam, H. P., Chen, E. S. & Grewal, S. I. Transcriptional scaffolds for heterochromatin assembly. Cell 136, 610–614 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Moore, M. J. & Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700 (2009).

    Article  CAS  PubMed  Google Scholar 

  25. Davuluri, R. V., Suzuki, Y., Sugano, S., Plass, C. & Huang, T. H. The functional consequences of alternative promoter use in mammalian genomes. Trends Genet. 24, 167–177 (2008).

    Article  CAS  PubMed  Google Scholar 

  26. Perales, R. & Bentley, D. “Cotranscriptionality”: the transcription elongation complex as a nexus for nuclear transactions. Mol. Cell 36, 178–191 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Cooper, T. A., Wan, L. & Dreyfuss, G. RNA and disease. Cell 136, 777–793 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Maniatis, T. & Tasic, B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418, 236–243 (2002).

    Article  CAS  PubMed  Google Scholar 

  29. Wahl, M. C., Will, C. L. & Luhrmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701–718 (2009).

    Article  CAS  PubMed  Google Scholar 

  30. Lutz, C. S. Alternative polyadenylation: a twist on mRNA 3′ end formation. ACS Chem. Biol. 3, 609–617 (2008).

    Article  CAS  PubMed  Google Scholar 

  31. Bass, B. L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71, 817–846 (2002).

    Article  CAS  PubMed  Google Scholar 

  32. Terns, M. & Terns, R. Noncoding RNAs of the H/ACA family. Cold Spring Harb. Symp. Quant. Biol. 71, 395–405 (2006).

    Article  CAS  PubMed  Google Scholar 

  33. Rottman, F. M., Bokar, J. A., Narayan, P., Shambaugh, M. E. & Ludwiczak, R. N6-adenosine methylation in mRNA: substrate specificity and enzyme complexity. Biochimie 76, 1109–1114 (1994).

    Article  CAS  PubMed  Google Scholar 

  34. Guschina, E. & Benecke, B. J. Specific and non-specific mammalian RNA terminal uridylyl transferases. Biochim. Biophys. Acta 1779, 281–285 (2008).

    Article  CAS  PubMed  Google Scholar 

  35. Martin, G. & Keller, W. RNA-specific ribonucleotidyl transferases. RNA 13, 1834–1849 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Sonenberg, N. & Hinnebusch, A. G. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136, 731–745 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Kochetov, A. V. Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays 30, 683–691 (2008).

    Article  CAS  PubMed  Google Scholar 

  38. Rodriguez, A. J., Czaplinski, K., Condeelis, J. S. & Singer, R. H. Mechanisms and cellular roles of local protein synthesis in mammalian cells. Curr. Opin. Cell Biol. 20, 144–149 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Houseley, J. & Tollervey, D. The many pathways of RNA degradation. Cell 136, 763–776 (2009).

    Article  CAS  PubMed  Google Scholar 

  40. Richter, J. D. Breaking the code of polyadenylation-induced translation. Cell 132, 335–337 (2008).

    Article  CAS  PubMed  Google Scholar 

  41. Chen, M. & Manley, J. L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nature Rev. Mol. Cell Biol. 10, 741–754 (2009).

    Article  CAS  Google Scholar 

  42. Zhao, J., Hyman, L. & Moore, C. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63, 405–445 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Mandel, C. R., Bai, Y. & Tong, L. Protein factors in pre-mRNA 3′-end processing. Cell. Mol. Life Sci. 65, 1099–1122 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Manley, J. L. & Takagaki, Y. The end of the message — another link between yeast and mammals. Science 274, 1481–1482 (1996).

    Article  CAS  PubMed  Google Scholar 

  45. Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Zhang, H., Lee, J. Y. & Tian, B. Biased alternative polyadenylation in human tissues. Genome Biol. 6, R100 (2005).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002).

    Article  CAS  PubMed  Google Scholar 

  49. Martin, K. C. & Ephrussi, A. mRNA localization: gene expression in the spatial dimension. Cell 136, 719–730 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Kornblihtt, A. R. Promoter usage and alternative splicing. Curr. Opin. Cell Biol. 17, 262–268 (2005).

    Article  CAS  PubMed  Google Scholar 

  51. Johnson, J. M. et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302, 2141–2144 (2003).

    Article  CAS  PubMed  Google Scholar 

  52. Sugnet, C. W. et al. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput. Biol. 2, e4 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  53. Ule, J. et al. Nova regulates brain-specific splicing to shape the synapse. Nature Genet. 37, 844–852 (2005). This study shows that NOVA2 regulates the splicing of transcripts that encode a biologically coherent set of proteins with synaptic localization and function.

    Article  CAS  PubMed  Google Scholar 

  54. Clark, T. A. et al. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol. 8, R64 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Johnson, J. M., Edwards, S., Shoemaker, D. & Schadt, E. E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21, 93–102 (2005).

    Article  CAS  PubMed  Google Scholar 

  56. Kapranov, P., Willingham, A. T. & Gingeras, T. R. Genome-wide transcription and the implications for genomic organization. Nature Rev. Genet. 8, 413–423 (2007).

    Article  CAS  PubMed  Google Scholar 

  57. Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916–919 (2002).

    Article  CAS  PubMed  Google Scholar 

  58. Seila, A. C., Core, L. J., Lis, J. T. & Sharp, P. A. Divergent transcription: a new feature of active promoters. Cell Cycle 8, 2557–2564 (2009).

    Article  CAS  PubMed  Google Scholar 

  59. Blencowe, B. J., Ahmad, S. & Lee, L. J. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 23, 1379–1386 (2009).

    Article  CAS  PubMed  Google Scholar 

  60. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genet. 10, 57–63 (2009).

    Article  CAS  PubMed  Google Scholar 

  61. Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genet. 40, 1413–1415 (2008).

    Article  CAS  PubMed  Google Scholar 

  62. Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Li, J. B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210–1213 (2009).

    Article  CAS  PubMed  Google Scholar 

  64. Porreca, G. J. et al. Multiplex amplification of large sets of human exons. Nature Methods 4, 931–936 (2007).

    Article  CAS  PubMed  Google Scholar 

  65. Lerner, M. R., Boyle, J. A., Mount, S. M., Wolin, S. L. & Steitz, J. A. Are snRNPs involved in splicing? Nature 283, 220–224 (1980).

    Article  CAS  PubMed  Google Scholar 

  66. Logan, J., Falck-Pedersen, E., Darnell, J. E. J. & Shenk, T. A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. Proc. Natl Acad. Sci. USA 84, 8306–8310 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Proudfoot, N. J. & Brownlee, G. G. 3′ non-coding region sequences in eukaryotic messenger RNA. Nature 263, 211–214 (1976).

    Article  CAS  PubMed  Google Scholar 

  68. Patel, A. A. & Steitz, J. A. Splicing double: insights from the second spliceosome. Nature Rev. Mol. Cell Biol. 4, 960–970 (2003).

    Article  CAS  Google Scholar 

  69. Castle, J. C. et al. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nature Genet. 40, 1416–1425 (2008).

    Article  CAS  PubMed  Google Scholar 

  70. Sorek, R. & Ast, G. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 13, 1631–1637 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Yeo, G. W., Van Nostrand, E., Holste, D., Poggio, T. & Burge, C. B. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl Acad. Sci. USA 102, 2850–2855 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Zhang, C. et al. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev. 22, 2550–2563 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Ast, G. How did alternative splicing evolve? Nature Rev. Genet. 5, 773–782 (2004).

    Article  CAS  PubMed  Google Scholar 

  74. Lareau, L. F., Inada, M., Green, R. E., Wengrod, J. C. & Brenner, S. E. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446, 926–929 (2007). This study reveals the presence of conserved elements and regulatory loops involved in NMD-coupled alternative splicing, which controls SR protein abundance.

    Article  CAS  PubMed  Google Scholar 

  75. Darnell, J. C., Mostovetsky, O. & Darnell, R. B. FMRP RNA targets: identification and validation. Genes Brain Behav. 4, 341–349 (2005).

    Article  CAS  PubMed  Google Scholar 

  76. Moore, M. J. & Silver, P. A. Global analysis of mRNA splicing. RNA 14, 197–203 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Tenenbaum, S. A., Carson, C. C., Lager, P. J. & Keene, J. D. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl Acad. Sci. USA 97, 14085–14090 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Darnell, R. B. Developing global insight into RNA regulation. Cold Spring Harb. Symp. Quant. Biol. 71, 321–327 (2006).

    Article  CAS  PubMed  Google Scholar 

  79. Kirino, Y. & Mourelatos, Z. Site-specific crosslinking of human microRNPs to RNA targets. RNA 14, 2254–2259 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Mili, S. & Steitz, J. A. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 10, 1692–1694 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Jensen, K. B. & Darnell, R. B. CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol. Biol. 488, 85–98 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Ule, J., Jensen, K., Mele, A. & Darnell, R. B. CLIP: a method for identifying protein–RNA interaction sites in living cells. Methods 37, 376–386 (2005).

    Article  CAS  PubMed  Google Scholar 

  83. Schoemaker, H. J. & Schimmel, P. R. Photo-induced joining of a transfer RNA with its cognate aminoacyl-transfer RNA synthetase. J. Mol. Biol. 84, 503–513 (1974).

    Article  CAS  PubMed  Google Scholar 

  84. Wagenmakers, A. J., Reinders, R. J. & van Venrooij, W. J. Cross-linking of mRNA to proteins by irradiation of intact cells with ultraviolet light. Eur. J. Biochem. 112, 323–330 (1980).

    Article  CAS  PubMed  Google Scholar 

  85. Economidis, I. V. & Pederson, T. Structure of nuclear ribonucleoprotein: heterogeneous nuclear RNA is complexed with a major sextet of proteins in vivo. Proc. Natl Acad. Sci. USA 80, 1599–1602 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Mayrand, S., Setyono, B., Greenberg, J. R. & Pederson, T. Structure of nuclear ribonucleoprotein: identification of proteins in contact with poly(A)+ heterogeneous nuclear RNA in living HeLa cells. J. Cell Biol. 90, 380–384 (1981).

    Article  CAS  PubMed  Google Scholar 

  87. Dreyfuss, G., Choi, Y. D. & Adam, S. A. Characterization of heterogeneous nuclear RNA–protein complexes in vivo with monoclonal antibodies. Mol. Cell Biol. 4, 1104–1114 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. Licatalosi, D. D. et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464–469 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Wang, Z., Tollervey, J., Briese, M., Turner, D. & Ule, J. CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods 48, 287–293 (2009).

    Article  PubMed  CAS  Google Scholar 

  90. Yeo, G. W. et al. An RNA code for the FOX2 splicing regulator revealed by mapping RNA–protein interactions in stem cells. Nature Struct. Mol. Biol. 16, 130–137 (2009).

    Article  CAS  Google Scholar 

  91. Chi, S. W., Zang, J. B., Mele, A. & Darnell, R. B. Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. Nature 460, 479–486 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Ule, J. et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 302, 1212–1215 (2003).

    Article  CAS  PubMed  Google Scholar 

  93. Sanford, J. R. et al. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 19, 381–394 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Licatalosi, D. D. & Darnell, R. B. Splicing regulation in neurologic disease. Neuron 52, 93–101 (2006).

    Article  CAS  PubMed  Google Scholar 

  95. Ule, J. & Darnell, R. B. RNA binding proteins and the regulation of neuronal synaptic plasticity. Curr. Opin. Neurobiol. 16, 102–110 (2006).

    Article  CAS  PubMed  Google Scholar 

  96. Wang, G. S. & Cooper, T. A. Splicing in disease: disruption of the splicing code and the decoding machinery. Nature Rev. Genet. 8, 749–761 (2007).

    Article  CAS  PubMed  Google Scholar 

  97. Kalsotra, A. et al. A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. Proc. Natl Acad. Sci. USA 105, 20333–20338 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Xu, Q., Modrek, B. & Lee, C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res. 30, 3754–3766 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Li, Q., Lee, J. A. & Black, D. L. Neuronal regulation of alternative pre-mRNA splicing. Nature Rev. Neurosci. 8, 819–831 (2007).

    Article  CAS  Google Scholar 

  100. Hattori, D., Millard, S. S., Wojtowicz, W. M. & Zipursky, S. L. Dscam-mediated cell recognition regulates neural circuit formation. Annu. Rev. Cell Dev. Biol. 24, 597–620 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Olson, S. et al. A regulator of Dscam mutually exclusive splicing fidelity. Nature Struct. Mol. Biol. 14, 1134–1140 (2007).

    Article  CAS  Google Scholar 

  102. Missler, M. & Sudhof, T. C. Neurexins: three genes and 1001 products. Trends Genet. 14, 20–26 (1998).

    Article  CAS  PubMed  Google Scholar 

  103. Boucard, A. A., Chubykin, A. A., Comoletti, D., Taylor, P. & Sudhof, T. C. A splice code for trans-synaptic cell adhesion mediated by binding of neuroligin 1 to α- and β-neurexins. Neuron 48, 229–236 (2005). This study reveals that the interaction of proteins across the synaptic cleft is driven by specific combinations of variants generated by alternative splicing.

    Article  CAS  PubMed  Google Scholar 

  104. Birzele, F., Csaba, G. & Zimmer, R. Alternative splicing and protein structure evolution. Nucleic Acids Res. 36, 550–558 (2008).

    Article  CAS  PubMed  Google Scholar 

  105. Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. & Burge, C. B. Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320, 1643–1647 (2008). This study shows that mRNA 3′ UTR length can be dynamically regulated in response to cell stimulation, allowing the escape of mRNAs from post-transcriptional control.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Mayr, C. & Bartel, D. P. Widespread shortening of 3′ UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673–684 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Lejeune, F. & Maquat, L. E. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 17, 309–315 (2005).

    Article  CAS  PubMed  Google Scholar 

  108. Lewis, B. P., Green, R. E. & Brenner, S. E. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl Acad. Sci. USA 100, 189–192 (2003).

    Article  CAS  PubMed  Google Scholar 

  109. Saltzman, A. L. et al. Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol. Cell Biol. 28, 4320–4330 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Boutz, P. L. et al. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 21, 1636–1652 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Makeyev, E. V., Zhang, J., Carrasco, M. A. & Maniatis, T. The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol. Cell 27, 435–448 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Wollerton, M. C., Gooding, C., Wagner, E. J., Garcia-Blanco, M. A. & Smith, C. W. Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol. Cell 13, 91–100 (2004).

    Article  CAS  PubMed  Google Scholar 

  113. Ni, J. Z. et al. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 21, 708–718 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Yu, Y. et al. Dynamic regulation of alternative splicing by silencers that modulate 5′ splice site competition. Cell 135, 1224–1236 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Caceres, J. F., Stamm, S., Helfan, D. M. & Krainer, A. R. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science 265, 1706–1709 (1994).

    Article  CAS  PubMed  Google Scholar 

  116. Ge, H. & Manley, J. L. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell 62, 25–34 (1990).

    Article  CAS  PubMed  Google Scholar 

  117. Krainer, A. R., Conway, G. C. & Kozak, D. The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell 62, 35–42 (1990).

    Article  CAS  PubMed  Google Scholar 

  118. Biamonti, G. & Caceres, J. F. Cellular stress and RNA splicing. Trends Biochem. Sci. 34, 146–153 (2009).

    Article  CAS  PubMed  Google Scholar 

  119. Feng, Y., Chen, M. & Manley, J. L. Phosphorylation switches the general splicing repressor SRp38 to a sequence-specific activator. Nature Struct. Mol. Biol. 15, 1040–1048 (2008). This study shows how post-translational regulation of a RNABP can alter its functional properties.

    Article  CAS  Google Scholar 

  120. Markovtsov, V. et al. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein. Mol. Cell Biol. 20, 7463–7479 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Polydorides, A. D., Okano, H. J., Yang, Y. Y., Stefani, G. & Darnell, R. B. 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 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Spellman, R., Llorian, M. & Smith, C. W. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol. Cell 27, 420–434 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Okano, H. J. & Darnell, R. B. A hierarchy of Hu RNA binding proteins in developing and adult neurons. J. Neurosci. 17, 3024–3037 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Vicente, M. et al. Muscleblind isoforms are functionally distinct and regulate α-actinin splicing. Differentiation 75, 427–440 (2007).

    Article  CAS  PubMed  Google Scholar 

  125. Matlin, A. J., Clark, F. & Smith, C. W. Understanding alternative splicing: towards a cellular code. Nature Rev. Mol. Cell Biol. 6, 386–398 (2005).

    Article  CAS  Google Scholar 

  126. Wang, Z. & Burge, C. B. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14, 802–813 (2008). This study uses RNA–seq and bioinformatics analyses to investigate potential mechanisms by which RNA processing events are coordinately regulated in different tissues.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Keene, J. D. RNA regulons: coordination of post-transcriptional events. Nature Rev. Genet. 8, 533–543 (2007).

    Article  CAS  PubMed  Google Scholar 

  128. Grosso, A. R. et al. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res. 36, 4823–4832 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Das, D. et al. A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res. 35, 4845–4857 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Fagnani, M. et al. Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol. 8, R108 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  131. Hu, J., Lutz, C. S., Wilusz, J. & Tian, B. Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11, 1485–1493 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Jelen, N., Ule, J., Zivin, M. & Darnell, R. B. Evolution of Nova-dependent splicing regulation in the brain. PLoS Genet. 3, 1838–1847 (2007).

    Article  CAS  PubMed  Google Scholar 

  133. Feng, Y. et al. SRp38 regulates alternative splicing and is required for Ca2+ handling in the embryonic heart. Dev. Cell 16, 528–538 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Ule, J. et al. An RNA map predicting Nova-dependent splicing regulation. Nature 444, 580–586 (2006).

    Article  CAS  PubMed  Google Scholar 

  135. Xu, X. et al. ASF/SF2-regulated CaMKIIδ alternative splicing temporally reprograms excitation–contraction coupling in cardiac muscle. Cell 120, 59–72 (2005).

    Article  CAS  PubMed  Google Scholar 

  136. Calarco, J. A. et al. Regulation of vertebrate nervous system-specific alternative splicing and development by an SR-related protein. Cell 138, 898–910 (2009).

    Article  CAS  PubMed  Google Scholar 

  137. Aznarez, I. et al. A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res. 18, 1247–1258 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Blanchette, M. et al. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol. Cell 33, 438–449 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Venables, J. P. et al. Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol. Cell Biol. 28, 6033–6043 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Dredge, B. K. & Darnell, R. B. Nova regulates GABAA receptor γ2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mol. Cell. Biol. 23, 4687–4700 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Dredge, B. K., Stefani, G., Engelhard, C. C. & Darnell, R. B. Nova autoregulation reveals dual functions in neuronal splicing. EMBO J. 24, 1608–1620 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Jensen, K. B. et al. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron 25, 359–371 (2000).

    Article  CAS  PubMed  Google Scholar 

  143. Guil, S. & Caceres, J. F. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nature Struct. Mol. Biol. 14, 591–596 (2007).

    Article  CAS  Google Scholar 

  144. Michlewski, G., Guil, S., Semple, C. A. & Caceres, J. F. Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol. Cell 32, 383–393 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D. & Brown, P. O. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 6, e255 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  146. Huang, C. S. et al. Common molecular pathways mediate long-term potentiation of synaptic excitation and slow synaptic inhibition. Cell 123, 105–118 (2005).

    Article  CAS  PubMed  Google Scholar 

  147. Ruggiu, M. et al. 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 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Kanadia, R. N., Clark, V. E., Punzo, C., Trimarchi, J. M. & Cepko, C. L. Temporal requirement of the alternative-splicing factor Sfrs1 for the survival of retinal neurons. Development 135, 3923–3933 (2008).

    Article  CAS  PubMed  Google Scholar 

  149. O'Rourke, J. R. & Swanson, M. S. Mechanisms of RNA-mediated disease. J. Biol. Chem. 284, 7419–7423 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Lagier-Tourenne, C. & Cleveland, D. W. Rethinking ALS: the FUS about TDP-43. Cell 136, 1001–1004 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Darnell, R. B. & Posner, J. B. Paraneoplastic syndromes involving the nervous system. N. Engl. J. Med. 349, 1543–1554 (2003).

    Article  CAS  PubMed  Google Scholar 

  152. Grohmann, K. et al. Mutations in the gene encoding immunoglobulin μ-binding protein 2 cause spinal muscular atrophy with respiratory distress type 1. Nature Genet. 29, 75–77 (2001).

    Article  CAS  PubMed  Google Scholar 

  153. Chen, Y. Z. et al. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Am. J. Hum. Genet. 74, 1128–1135 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Antonellis, A. et al. Glycyl tRNA synthetase mutations in Charcot–Marie–Tooth disease type 2D and distal spinal muscular atrophy type V. Am. J. Hum. Genet. 72, 1293–1299 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Grosso, A. R., Martins, S. & Carmo-Fonseca, M. The emerging role of splicing factors in cancer. EMBO Rep. 9, 1087–1093 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Venables, J. P. et al. Cancer-associated regulation of alternative splicing. Nature Struct. Mol. Biol. 16, 670–676 (2009). This study combined bioinformatics and functional studies to establish a link between splicing deregulation and cancer.

    Article  CAS  Google Scholar 

  157. Karni, R. et al. The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nature Struct. Mol. Biol. 14, 185–193 (2007).

    Article  CAS  Google Scholar 

  158. Richter, J. D. & Klann, E. Making synaptic plasticity and memory last: mechanisms of translational regulation. Genes Dev. 23, 1–11 (2009).

    Article  CAS  PubMed  Google Scholar 

  159. Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Doyle, J. P. et al. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135, 749–762 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Heiman, M. et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738–748 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature Methods 6, 377–382 (2009).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We are grateful to members of the laboratory for thoughtful discussions. We apologize to the many colleagues whose interesting studies we reviewed but were unable to cite here due to space limitations. This work was supported by grants from the National Institute of Health and the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Robert B. Darnell.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

FURTHER INFORMATION

Robert Darnell's homepage

Nature Reviews Genetics article series on Applications of Next-generation Sequencing

Glossary

R-loop

A hybrid structure consisting of RNA and DNA in which RNA displaces a DNA strand to hybridize to its complementary DNA sequence. The formation of R-loops was a key method to define the relationship between genes and their RNA products.

'RNA World' hypothesis

A hypothesis that life originated as an RNA-based form, based on the finding that RNA can act as both genetic material and an enzyme.

Piwi-interacting RNA

A small RNA species that is processed from a single-stranded precursor RNA. They are 25–35 nucleotides in length and form complexes with the piwi protein. piRNAs are thought to have roles in transposon silencing and stem cell function.

RNA editing

The post-transcriptional modification of RNA primary sequence by the insertion and/or deletion of specific bases, or the chemical modification of adenosine to inosine or cytidine to uridine.

Exon-junction microarray

A microarray platform that contains probe sets designed to detect the mRNA sequences (junctions) formed by the splicing of one exon to another.

Ultraconserved element

A large sequence in the genome (usually >200 nucleotides) that shows high levels of conservation across multiple species.

Nonsense-mediated decay

The process by which mRNAs containing premature termination codons are destroyed to preclude the production of truncated and potentially deleterious protein products. It is also used in combination with specific alternative splicing events to control the levels of some proteins.

Morpholino

An oligomer of 25 nucleotides with bases linked to a morpholine ring. The oligomers can bind and inactivate selected RNA sequences on the basis of base pairing and steric interference.

Small interfering RNA

RNA molecules that are 21–23 nucleotides long and that are processed from long double-stranded RNAs. They are functional components of the RNAi-induced silencing complex. They typically target and silence mRNAs by binding perfectly complementary sequences in the mRNA and causing their degradation and/or translation inhibition.

Exon skipping

Exclusion of an exon from the resulting mature mRNA due to direct splicing of the upstream exon to the downstream exon.

Seed site

A short RNA sequence that is bound by and necessary for microRNA-mediated RNA regulation.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Licatalosi, D., Darnell, R. RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11, 75–87 (2010). https://doi.org/10.1038/nrg2673

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrg2673

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing