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.

  • Review Article
  • Published:

The physiology of alternative splicing

Nature Reviews Molecular Cell Biology volume 24, pages 242–254 (2023)Cite this article

Subjects

Abstract

Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Principles of alternative splicing.
Fig. 2: Examples of biologically relevant alternative splicing and its mode of regulation.
Fig. 3: Protein variants arising from alternative splicing.
Fig. 4: Binary splicing switches.
Fig. 5: Therapeutic modulation of alternative splicing.

Similar content being viewed by others

References

  1. 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 

  2. 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 

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

    Article  CAS  PubMed  Google Scholar 

  4. Khan, M. R., Wellinger, R. J. & Laurent, B. Exploring the alternative splicing of long noncoding RNAs. Trends Genet. 37, 695–698 (2021).

    Article  CAS  PubMed  Google Scholar 

  5. Rogers, S. O. Integrated evolution of ribosomal RNAs, introns, and intron nurseries. Genetica 147, 103–119 (2019).

    Article  CAS  PubMed  Google Scholar 

  6. Sekulovski, S. et al. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia. Nat. Commun. 12, 5610 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kearse, M. G. & Wilusz, J. E. Non-AUG translation: a new start for protein synthesis in eukaryotes. Genes Dev. 31, 1717–1731 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Smith, C. W. & Valcárcel, J. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. 25, 381–388 (2000).

    Article  CAS  PubMed  Google Scholar 

  9. Kastner, B., Will, C. L., Stark, H. & Lührmann, R. Structural insights into nuclear pre-mRNA splicing in higher eukaryotes. Cold Spring Harb. Perspect. Biol. 11, a032417 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Licatalosi, D. D. & Darnell, R. B. RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet. 11, 75–87 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Irimia, M. & Blencowe, B. J. Alternative splicing: decoding an expansive regulatory layer. Curr. Opin. Cell Biol. 24, 323–332 (2012).

    Article  CAS  PubMed  Google Scholar 

  12. Kornblihtt, A. R. et al. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell Biol. 14, 153–165 (2013).

    Article  CAS  PubMed  Google Scholar 

  13. Fu, X.-D. & Ares, M. Context-dependent control of alternative splicing by RNA-binding proteins. Nat. Rev. Genet. 15, 689–701 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Baralle, F. E. & Giudice, J. Alternative splicing as a regulator of development and tissue identity. Nat. Rev. Mol. Cell Biol. 18, 437–451 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ule, J. & Blencowe, B. J. Alternative splicing regulatory networks: functions, mechanisms, and evolution. Mol. Cell 76, 329–345 (2019).

    Article  CAS  PubMed  Google Scholar 

  16. Shenasa, H. & Hertel, K. J. Combinatorial regulation of alternative splicing. Biochim. Biophys. Acta Gene Regul. Mech. 1862, 194392 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Gordon, J. M., Phizicky, D. V. & Neugebauer, K. M. Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision.Curr. Opin. Genet. Dev. 67, 67–76 (2021).

    Article  CAS  PubMed  Google Scholar 

  18. Buratti, E., Baralle, M. & Baralle, F. E. From single splicing events to thousands: the ambiguous step forward in splicing research. Brief. Funct. Genomics 12, 3–12 (2013).

    Article  CAS  PubMed  Google Scholar 

  19. 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. Nat. Genet. 40, 1413–1415 (2008).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Saldi, T., Riemondy, K., Erickson, B. & Bentley, D. L. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Mol. Cell 81, 1789–1801.e5 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Luco, R. F., Allo, M., Schor, I. E., Kornblihtt, A. R. & Misteli, T. Epigenetics in alternative pre-mRNA splicing. Cell 144, 16–26 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. de la Mata, M. et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12, 525–532 (2003).

    Article  PubMed  Google Scholar 

  24. Dujardin, G. et al. How slow RNA polymerase II elongation favors alternative exon skipping. Mol. Cell 54, 683–690 (2014).

    Article  CAS  PubMed  Google Scholar 

  25. Fong, N. et al. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev. 28, 2663–2676 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Maslon, M. M. et al. A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes. EMBO J. 38, e101244 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  27. Schor, I. E., Rascovan, N., Pelisch, F., Alló, M. & Kornblihtt, A. R. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl Acad. Sci. USA 106, 4325–4330 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Alló, M. et al. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol. 16, 717–724 (2009).

    Article  PubMed  Google Scholar 

  29. Schor, I. E., Fiszbein, A., Petrillo, E. & Kornblihtt, A. R. Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation. EMBO J. 32, 2264–2274 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Segelle, A. et al. Histone marks regulate the epithelial-to-mesenchymal transition via alternative splicing. Cell Rep. 38, 110357 (2022).

    Article  CAS  PubMed  Google Scholar 

  31. Eling, N., Morgan, M. D. & Marioni, J. C. Challenges in measuring and understanding biological noise. Nat. Rev. Genet. 20, 536–548 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Tress, M. L., Abascal, F. & Valencia, A. Most alternative isoforms are not functionally important. Trends Biochem. Sci. 42, 98–110 (2017).

    Article  CAS  PubMed  Google Scholar 

  33. Rodriguez, J. M., Pozo, F., di Domenico, T., Vazquez, J. & Tress, M. L. An analysis of tissue-specific alternative splicing at the protein level. PLoS Comput. Biol. 16, e1008287 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Pozo, F. et al. Assessing the functional relevance of splice isoforms. NAR Genomics Bioinform 3, lqab044 (2021).

    Article  Google Scholar 

  35. Blencowe, B. J. The relationship between alternative splicing and proteomic complexity. Trends Biochem. Sci. 42, 407–408 (2017).

    Article  CAS  PubMed  Google Scholar 

  36. Ingolia, N. T. Ribosome footprint profiling of translation throughout the genome. Cell 165, 22–33 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Weatheritt, R. J., Sterne-Weiler, T. & Blencowe, B. J. The ribosome-engaged landscape of alternative splicing. Nat. Struct. Mol. Biol. 23, 1117–1123 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Kurosaki, T. & Maquat, L. E. Nonsense-mediated mRNA decay in humans at a glance. J. Cell Sci. 129, 461–467 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Floor, S. N. & Doudna, J. A. Tunable protein synthesis by transcript isoforms in human cells. eLife 5, e10921 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Sterne-Weiler, T. et al. Frac-seq reveals isoform-specific recruitment to polyribosomes. Genome Res. 23, 1615–1623 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Xing, Y. & Lee, C. Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet. 7, 499–509 (2006).

    Article  CAS  PubMed  Google Scholar 

  42. Bell, L. R., Horabin, J. I., Schedl, P. & Cline, T. W. Positive autoregulation of Sex-lethal by alternative splicing maintains the female determined state in Drosophila. Cell 65, 229–239 (1991).

    Article  CAS  PubMed  Google Scholar 

  43. Gracheva, E. O. et al. Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats. Nature 476, 88–91 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  45. Peterson, M. L. Immunoglobulin heavy chain gene regulation through polyadenylation and splicing competition. Wiley Interdiscip. Rev. RNA 2, 92–105 (2011).

    Article  CAS  PubMed  Google Scholar 

  46. Hattori, D. et al. Robust discrimination between self and non-self neurites requires thousands of Dscam1 isoforms. Nature 461, 644–648 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Emery, A. & Swanstrom, R. HIV-1: to splice or not to splice, that is the question. Viruses 13, 181–190 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Liu, Y., Beyer, A. & Aebersold, R. On the dependency of cellular protein levels on mRNA abundance. Cell 165, 535–550 (2016).

    Article  CAS  PubMed  Google Scholar 

  49. El Marabti, E. & Younis, I. The cancer spliceome: reprograming of alternative splicing in cancer. Front. Mol. Biosci. 5, 80 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Bangru, S. et al. Alternative splicing rewires Hippo signaling pathway in hepatocytes to promote liver regeneration. Nat. Struct. Mol. Biol. 25, 928–939 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Jensen, M. A., Wilkinson, J. E. & Krainer, A. R. Splicing factor SRSF6 promotes hyperplasia of sensitized skin. Nat. Struct. Mol. Biol. 21, 189–197 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Anczuków, O. & Krainer, A. R. Splicing-factor alterations in cancers. RNA 22, 1285–1301 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Cherry, S. & Lynch, K. W. Alternative splicing and cancer: insights, opportunities, and challenges from an expanding view of the transcriptome. Genes Dev. 34, 1005–1016 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Gurnari, C., Pagliuca, S. & Visconte, V. Alternative splicing in myeloid malignancies. Biomedicines 9, 1844–1851 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Das, S., Anczuków, O., Akerman, M. & Krainer, A. R. Oncogenic splicing factor SRSF1 is a critical transcriptional target of MYC. Cell Rep. 1, 110–117 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Rahman, M. A., Lin, K.-T., Bradley, R. K., Abdel-Wahab, O. & Krainer, A. R. Recurrent SRSF2 mutations in MDS affect both splicing and NMD. Genes Dev. 34, 413–427 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Papasaikas, P., Tejedor, J. R., Vigevani, L. & Valcárcel, J. Functional splicing network reveals extensive regulatory potential of the core spliceosomal machinery. Mol. Cell 57, 7–22 (2015).

    Article  CAS  PubMed  Google Scholar 

  59. Saltzman, A. L., Pan, Q. & Blencowe, B. J. Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev. 25, 373–384 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Pleiss, J. A., Whitworth, G. B., Bergkessel, M. & Guthrie, C. Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol. 5, e90 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  61. Radzisheuskaya, A. et al. PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia. Nat. Struct. Mol. Biol. 26, 992–1012 (2019).

    Article  Google Scholar 

  62. Braun, C. J. et al. Coordinated splicing of regulatory detained introns within oncogenic transcripts creates an exploitable vulnerability in malignant glioma. Cancer Cell 32, 411–426.e11 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Sanford, J. R., Gray, N. K., Beckmann, K. & Cáceres, J. F. A novel role for shuttling SR proteins in mRNA translation. Genes Dev. 18, 755–768 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Haward, F. et al. Nucleo-cytoplasmic shuttling of splicing factor SRSF1 is required for development and cilia function. eLife 10, e65104 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Munkley, J. et al. Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer. eLife 8, e47678 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Irimia, M. et al. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159, 1511–1523 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Ellis, J. D. et al. Tissue-specific alternative splicing remodels protein–protein interaction networks. Mol. Cell 46, 884–892 (2012).

    Article  CAS  PubMed  Google Scholar 

  68. Buljan, M. et al. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol. Cell 46, 871–883 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Gonatopoulos-Pournatzis, T. et al. Autism-misregulated eIF4G microexons control synaptic translation and higher order cognitive functions. Mol. Cell 77, 1176–1192.e16 (2020).

    Article  CAS  PubMed  Google Scholar 

  70. Parras, A. et al. Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing. Nature 560, 441–446 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Sharon, G. et al. Human gut microbiota from autism spectrum disorder promote behavioral symptoms in mice. Cell 177, 1600–1618 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Haltenhof, T. et al. A conserved kinase-based body-temperature sensor globally controls alternative splicing and gene expression. Mol. Cell 78, 57–69 (2020).

    Article  CAS  PubMed  Google Scholar 

  73. Martin Anduaga, A. et al. Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. eLife 8, e44642 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  74. Barbosa-Morais, N. L. et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 338, 1587–1593 (2012).

    Article  CAS  PubMed  Google Scholar 

  75. Merkin, J., Russell, C., Chen, P. & Burge, C. B. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338, 1593–1599 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Gueroussov, S. et al. An alternative splicing event amplifies evolutionary differences between vertebrates. Science 349, 868–873 (2015).

    Article  CAS  PubMed  Google Scholar 

  77. Guo, W. et al. RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing. Nat. Med. 18, 766–773 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Murphy, P. A. et al. Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow. eLife 7, e29494 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  79. Vernia, S. et al. An alternative splicing program promotes adipose tissue thermogenesis. eLife 5, e17672 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  80. Marcheva, B. et al. A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. Genes Dev. 34, 1089–1105 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Ha, K. C. H., Sterne-Weiler, T., Morris, Q., Weatheritt, R. J. & Blencowe, B. J. Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity. Nat. Commun. 12, 335 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Leff, S. E., Evans, R. M. & Rosenfeld, M. G. Splice commitment dictates neuron-specific alternative RNA processing in calcitonin/CGRP gene expression. Cell 48, 517–524 (1987).

    Article  CAS  PubMed  Google Scholar 

  83. Schmucker, D. et al. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101, 671–684 (2000).

    Article  CAS  PubMed  Google Scholar 

  84. Graveley, B. R. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell 123, 65–73 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Goodman, K. M. et al. How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition. eLife 11, e72416 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Penev, A. et al. Alternative splicing is a developmental switch for hTERT expression. Mol. Cell 81, 2349–2360.e6 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Fiszbein, A. et al. Alternative splicing of G9a regulates neuronal differentiation. Cell Rep. 14, 2797–2808 (2016).

    Article  CAS  PubMed  Google Scholar 

  88. Gabut, M. et al. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell 147, 132–146 (2011).

    Article  CAS  PubMed  Google Scholar 

  89. Han, H. et al. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature 498, 241–245 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Choksi, A. et al. Tumor suppressor SMAR1 regulates PKM alternative splicing by HDAC6-mediated deacetylation of PTBP1. Cancer Metab. 9, 16–21 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  91. David, C. J., Chen, M., Assanah, M., Canoll, P. & Manley, J. L. hnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer. Nature 463, 364–368 (2010).

    Article  CAS  PubMed  Google Scholar 

  92. Mirtschink, P. et al. HIF-driven SF3B1 induces KHK-C to enforce fructolysis and heart disease. Nature 522, 444–449 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Li, G. et al. Exclusion of alternative exon 33 of Ca V 1.2 calcium channels in heart is proarrhythmogenic. Proc. Natl Acad. Sci. USA 114, E4288–E4295 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Sebastian, S. et al. Tissue-specific splicing of a ubiquitously expressed transcription factor is essential for muscle differentiation. Genes Dev. 27, 1247–1259 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Scharner, J. & Aznarez, I. Clinical applications of single-stranded oligonucleotides: current landscape of approved and in-development therapeutics. Mol. Ther. 29, 540–554 (2021).

    Article  CAS  PubMed  Google Scholar 

  96. Monani, U. R. The human centromeric survival motor neuron gene (SMN2) rescues embryonic lethality in Smn–/– mice and results in a mouse with spinal muscular atrophy. Hum. Mol. Genet. 9, 333–339 (2000).

    Article  CAS  PubMed  Google Scholar 

  97. Singh, N. K., Singh, N. N., Androphy, E. J. & Singh, R. N. Splicing of a critical exon of human Survival Motor Neuron is regulated by a unique silencer element located in the last intron. Mol. Cell. Biol. 26, 1333–1346 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Hua, Y., Vickers, T. A., Okunola, H. L., Bennett, C. F. & Krainer, A. R. Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am. J. Hum. Genet. 82, 834–848 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hua, Y. et al. Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model. Nature 478, 123–126 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Hua, Y. et al. Motor neuron cell-nonautonomous rescue of spinal muscular atrophy phenotypes in mild and severe transgenic mouse models. Genes Dev. 29, 288–297 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Chiriboga, C. A. et al. Results from a phase 1 study of nusinersen (ISIS-SMNRx) in children with spinal muscular atrophy. Neurology 86, 890–897 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Rigo, F. et al. Pharmacology of a central nervous system delivered 2′-O-methoxyethyl-modified survival of motor neuron splicing oligonucleotide in mice and nonhuman primates. J. Pharmacol. Exp. Ther. 350, 46–55 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  103. Marasco, L. E. et al. Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell 185, 2057–2070 (2022).

    Article  CAS  PubMed  Google Scholar 

  104. Darras, B. T. et al. Risdiplam-treated infants with type 1 spinal muscular atrophy versus historical controls. N. Engl. J. Med. 385, 427–435 (2021).

    Article  CAS  PubMed  Google Scholar 

  105. Arechavala-Gomeza, V. et al. Comparative analysis of antisense oligonucleotide sequences for targeted skipping of exon 51 during dystrophin pre-mRNA splicing in human muscle. Hum. Gene Ther. 18, 798–810 (2007).

    Article  CAS  PubMed  Google Scholar 

  106. Aartsma-Rus, A. et al. Development of exon skipping therapies for Duchenne muscular dystrophy: a critical review and a perspective on the outstanding issues. Nucleic Acid. Ther. 27, 251–259 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Koenig, M. et al. The molecular basis for duchenne versus becker muscular dystrophy: correlation of severity with type of deletion. Tha Am. J. Hum. Genet. 45, 498–506 (1989).

    CAS  Google Scholar 

  108. Wright, C. J., Smith, C. W. J. & Jiggins, C. D. Alternative splicing as a source of phenotypic diversity. Nat. Rev. Genet. https://doi.org/10.1038/s41576-022-00514-4 (2022).

    Article  PubMed  Google Scholar 

  109. Cunningham, F. et al. Ensembl 2019. Nucleic Acids Res. 47, D745–D751 (2019).

    Article  CAS  PubMed  Google Scholar 

  110. 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 

  111. Kovalak, C., Donovan, S., Bicknell, A. A., Metkar, M. & Moore, M. J. Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways. Genome Biol. 22, 132 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Keren, H., Lev-Maor, G. & Ast, G. Alternative splicing and evolution: diversification, exon definition and function. Nat. Rev. Genet. 11, 345–355 (2010).

    Article  CAS  PubMed  Google Scholar 

  113. Ashraf, U., Benoit-Pilven, C., Lacroix, V., Navratil, V. & Naffakh, N. Advances in analyzing virus-induced alterations of host cell splicing. Trends Microbiol. 27, 268–281 (2019).

    Article  CAS  PubMed  Google Scholar 

  114. Szakonyi, D. & Duque, P. Alternative splicing as a regulator of early plant development. Front. Plant. Sci. 9, 1174 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  115. Syed, N. H., Kalyna, M., Marquez, Y., Barta, A. & Brown, J. W. S. Alternative splicing in plants — coming of age. Trends Plant. Sci. 17, 616–623 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Godoy Herz, M. A. et al. Light regulates plant alternative splicing through the control of transcriptional elongation. Mol. Cell 73, 1066–1074 (2019).

    Article  CAS  PubMed  Google Scholar 

  117. Sanchez, S. E. et al. A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature 468, 112–116 (2010).

    Article  CAS  PubMed  Google Scholar 

  118. Fairbrother, W. G., Yeh, R.-F., Sharp, P. A. & Burge, C. B. Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007–1013 (2002).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors apologize to those researchers whose work could not be cited owing to space constraints. They thank B. Blencowe for critical reading of the manuscript and L. Giono for the design of Fig. 3B. Work in the authors’ laboratory was supported by a joint grant from Familias Atrofia Muscular Espinal (FAME, Argentina) and CureSMA (USA), and grants from the Lounsbery Foundation (USA), the Universidad de Buenos Aires (UBACYT 20020170100046BA), the Agencia Nacional de Promoción Científica y Tecnológica of Argentina (PICT-2019 862) and the CONICET (PUE 22920170100062CO).

Author information

Author notes

  1. Luciano E. Marasco

    Present address: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK

Authors and Affiliations

  1. Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina

    Luciano E. Marasco & Alberto R. Kornblihtt

Authors
  1. Luciano E. Marasco
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alberto R. Kornblihtt
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Both authors researched data for the article, made substantial contribution to discussion of content and reviewed and/or edited the manuscript before submission. A.R.K. wrote the manuscript.

Corresponding author

Correspondence to Alberto R. Kornblihtt.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Molecular Cell Biology thanks Jimena Giudice, Juan Valcárcel, and Leilei Chen, who co-reviewed with Han Jian, for their contribution to the peer review of this work.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related links

National Human Genome Research Institute, National Institutes of Health (NIH): https://www.genome.gov/genetics-glossary/Exon

Glossary

Transesterification

The exchange of the organic group R″ of an ester with the organic group R′ of an alcohol. In the second step of splicing, the uncleaved intron 3′ end is the (phosphodi)ester and the free exon is the alcohol. Following the reaction, the free intron becomes an alcohol and the joined exons form a phosphodiester bond.

Cassette exons

Exons that as a whole are either included in or skipped from the mature mRNA.

Class I exons

Exons whose inclusion in the mature mRNA is promoted by slow, and inhibited by fast, transcript elongation.

Class II exons

Exons whose inclusion in the mature mRNA is inhibited by slow, and promoted by fast, transcript elongation.

Nonsense-mediated decay

(NMD). An mRNA degradation mechanism that is coupled to splicing and translation and is triggered by premature stop codons.

Detained introns

Introns that cause the mRNAs that harbour them to remain in the nucleus.

γ-Aminobutyric acid A

(GABAA). A small organic molecule synthesized from the amino acid glutamic acid that acts as a neurotransmitter whose receptors are part of ligand-gated ion channels.

Peptidergic secretion

The secretion of small polypeptides with neurotransmitter activity.

Exon shuffling

A mechanism for the formation of new genes in eukaryotes during evolution, usually through recombination between introns of different genes, yielding novel rearranged genes with altered functions, without elimination of the original genes.

r-Selection

A type of evolutionary selective pressure. r-Selected species, such as bacteria, are small organisms with short life cycles and fast maturation that are able to rapidly populate new environments.

K-Selection

A type of evolutionary selective pressure. K-Selected species, such as pluricellular organisms with specialized tissues and organs, are bigger, have longer life cycles and slow maturation, and their colonization of new environments depends on their ability to adapt physiologically.

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Marasco, L.E., Kornblihtt, A.R. The physiology of alternative splicing. Nat Rev Mol Cell Biol 24, 242–254 (2023). https://doi.org/10.1038/s41580-022-00545-z

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41580-022-00545-z

This article is cited by

Search

Advanced 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