Abstract
The pre-mRNA splicing process is an essential aspect of gene expression and function and plays a substantial role in the complexity of higher eukaryotes. The development of antisense oligonucleotides (AOs) to harness the splicing process and manipulate it to treat various inherited and acquired diseases has been boosted by its flexibility and customisation capability. As the amount of research in this space increases, certain aspects need to be considered, in particular, how nonsequential splicing of pre-mRNA can impact AO-mediated splicing manipulation. In this chapter, we reviewed literature discussing intron removal order and several examples of disease-causing mutations impacted by this phenomenon. We also compared two strategies used to study intron removal order and the occasions that they are best suited. Finally, we discuss how nonsequential splicing could facilitate or impede the development of splice-manipulating AOs and aspects to consider when analysing AO effectiveness.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aartsma-Rus A, Bremmer-Bout M, Janson AA et al (2002) Targeted exon skipping as a potential gene correction therapy for Duchenne muscular dystrophy. Neuromuscul Disord 12(Suppl 1):S71-77
Aartsma-Rus A, Fokkema I, Verschuuren J et al (2009) Theoretic applicability of antisense-mediated exon skipping for Duchenne muscular dystrophy mutations. Hum Mutat 30:293–299
Adkin CF, Meloni PL, Fletcher S et al (2012) Multiple exon skipping strategies to by-pass dystrophin mutations. Neuromuscul Disord 22:297–305
Attanasio C, David A, Neerman-Arbez M (2003) Outcome of donor splice site mutations accounting for congenital afibrinogenemia reflects order of intron removal in the fibrinogen alpha gene (FGA). Blood 101:1851–1856
Aung-Htut MT, Comerford I, Johnsen R et al (2019) Reduction of integrin alpha 4 activity through splice modulating antisense oligonucleotides. Sci Rep 9:12994–13005
Baralle FE, Giudice J (2017) Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol 18:437–451
Baralle M, Skoko N, Knezevich A et al (2006) NF1 mRNA biogenesis: effect of the genomic milieu in splicing regulation of the NF1 exon 37 region. FEBS Lett 580:4449–4456
Berk AJ, Sharp PA (1977) Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12:721–732
Bradnam KR, Korf I (2008) Longer first introns are a general property of eukaryotic gene structure. PLoS ONE 3:e3093
Chelly J, Gilgenkrantz H, Lambert M et al (1990) Effect of dystrophin gene deletions on mRNA levels and processing in Duchenne and Becker muscular dystrophies. Cell 63:1239–1248
Chow LT, Roberts JM, Lewis JB et al (1977) A map of cytoplasmic RNA transcripts from lytic adenovirus type 2, determined by electron microscopy of RNA:DNA hybrids. Cell 11:819–836
Crooke ST, Baker BF, Crooke RM et al (2021) Antisense technology: an overview and prospectus. Nat Rev Drug Discov 20:427–453
De La Mata M, Alonso CR, Kadener S et al (2003) A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12:525–532
Den Dunnen JT, Grootscholten PM, Bakker E et al (1989) Topography of the Duchenne muscular dystrophy (DMD) gene: FIGE and cDNA analysis of 194 cases reveals 115 deletions and 13 duplications. Am J Hum Genet 45:835–847
Dominski Z, Kole R (1993) Restoration of correct splicing in thalassemic pre-mRNA by antisense oligonucleotides. Proc Natl Acad Sci USA 90:8673–8677
Echigoya Y, Lim KRQ, Melo D et al (2019) Exons 45–55 skipping using mutation-tailored cocktails of antisense morpholinos in the DMD gene. Mol Ther 27:2005–2017
Ferreiro V, Giliberto F, Muñiz GMN et al (2009) Asymptomatic Becker muscular dystrophy in a family with a multiexon deletion. Muscle Nerve 39:239–243
Fletcher S, Adkin CF, Meloni P et al (2012) Targeted exon skipping to address “leaky” mutations in the dystrophin gene. Mol Ther Nucleic Acids 1:e48
Fong N, Kim H, Zhou Y et al (2014) Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev 28:2663–2676
Fox-Walsh KL, Dou Y, Lam BJ et al (2005) The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 102:16176–16181
Gazzoli I, Pulyakhina I, Verwey NE et al (2016) Non-sequential and multi-step splicing of the dystrophin transcript. RNA Biol 13:290–305
Gudas JM, Knight GB, Pardee AB (1990) Ordered splicing of thymidine kinase pre-mRNA during the S phase of the cell cycle. Mol Cell Biol 10:5591–5595
Gumińska N, Płecha M, Zakryś B et al (2018) Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis. PLOS Genet 14:e1007761
Ham KA, Aung-Htut MT, Fletcher S et al (2020) Nonsequential splicing events alter antisense-mediated exon skipping outcome in COL7A1. Int J Mol Sci 21:7705–7719
Haque N, Oberdoerffer S (2014) Chromatin and splicing. Methods Mol Biol 1126:97–113
Havens MA, Hastings ML (2016) Splice-switching antisense oligonucleotides as therapeutic drugs. Nucleic Acids Res 44:6549–6563
Kadener S, Fededa JP, Rosbash M et al (2002) Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Proc Natl Acad Sci USA 99:8185–8190
Keegan NP (2020) Pseudoexons of the DMD gene. J Neuromuscul Dis 7:77–95
Kelemen O, Convertini P, Zhang Z et al (2013) Function of alternative splicing. Gene 514:1–30
Kessler O, Jiang Y, Chasin LA (1993) Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA. Mol Cell Biol 13:6211–6222
Kim SW, Taggart AJ, Heintzelman C et al (2017) Widespread intra-dependencies in the removal of introns from human transcripts. Nucleic Acids Res 45:9503–9513
Koenig M, Beggs AH, Moyer M et al (1989) The molecular basis for Duchenne versus Becker muscular dystrophy: correlation of severity with type of deletion. Am J Hum Genet 45:498–506
Lee Y, Rio DC (2015) Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem 84:291–323
Li D, Adams AM, Johnsen RD et al (2020) Morpholino oligomer-induced dystrophin isoforms to map the functional domains in the dystrophin protein. Mol Ther Nucleic Acids 22:263–272
Li D, McIntosh CS, Mastaglia FL et al (2021) Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener 10:16–33
Mann CJ, Honeyman K, Cheng AJ et al (2001) Antisense-induced exon skipping and synthesis of dystrophin in the mdx mouse. Proc Natl Acad Sci USA 98:42–47
McClorey G, Moulton HM, Iversen PL et al (2006) Antisense oligonucleotide-induced exon skipping restores dystrophin expression in vitro in a canine model of DMD. Gene Ther 13:1373–1381
Mitrpant C, Adams AM, Meloni PL et al (2009) Rational design of antisense oligomers to induce dystrophin exon skipping. Mol Ther 17:1418–1426
Neri M, Rossi R, Trabanelli C et al (2020) The genetic landscape of dystrophin mutations in Italy: a nationwide study. Front Genet 11:131–145
Nobile C, Marchi J, Nigro V et al (1997) Exon-intron organization of the human dystrophin gene. Genomics 45:421–424
Nogues G, Munoz MJ, Kornblihtt AR (2003) Influence of polymerase II processivity on alternative splicing depends on splice site strength. J Biol Chem 278:52166–52171
Noteborn M, Arnberg A, de Jonge M et al (1986) Splicing pathways of the chicken apo very low density lipoprotein II (pre)messenger RNA. FEBS Lett 194:151–156
Park E, Pan Z, Zhang Z et al (2018) The expanding landscape of alternative splicing variation in human populations. Am J Hum Genet 102:11–26
Pulyakhina I, Gazzoli I, t Hoen PA, et al (2015) SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing. Nucleic Acids Res 43:e80
Rodrigues M, Yokota T (2018) An overview of recent advances and clinical applications of exon skipping and splice modulation for muscular dystrophy and various genetic diseases. Springer, New York, pp 31–55
Saito M, Masunaga T, Ishiko A (2009) A novel de novo splice-site mutation in the COL7A1 gene in dominant dystrophic epidermolysis bullosa (DDEB): specific exon skipping could be a prognostic factor for DDEB pruriginosa. Clin Exp Dermatol 34:e934
Schor IE, Gomez Acuna LI, Kornblihtt AR (2013) Coupling between transcription and alternative splicing. Cancer Treat Res 158:1–24
Schwarze U, Starman BJ, Byers PH (1999) Redefinition of exon 7 in the COL1A1 gene of type I collagen by an intron 8 splice-donor-site mutation in a form of osteogenesis imperfecta: influence of intron splice order on outcome of splice-site mutation. Am J Hum Genet 65:336–344
Shukla S, Oberdoerffer S (2012) Co-transcriptional regulation of alternative pre-mRNA splicing. Biochim Biophys Acta 1819:673–683
Sperling R (2017) The nuts and bolts of the endogenous spliceosome. Wires RNA 8:e1377
Takahara K, Schwarze U, Imamura Y et al (2002) Order of intron removal influences multiple splice outcomes, including a two-exon skip, in a COL5A1 acceptor-site mutation that results in abnormal pro-α1(V) N-propeptides and Ehlers-Danlos syndrome type I. Am J Hum Genet 71:451–465
Tennyson CN, Klamut HJ, Worton RG (1995) The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat Genet 9:184–190
Tsai M-J, Ting AC, Nordstrom JL et al (1980) Processing of high molecular weight ovalbumin and ovomucoid precursor RNAs to messenger RNA. Cell 22:219–230
Van Vliet L, De Winter CL, Van Deutekom JC et al (2008) Assessment of the feasibility of exon 45–55 multiexon skipping for duchenne muscular dystrophy. BMC Med Genet 9:105–111
Wahl MC, Will CL, Luhrmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136:701–718
Walsh PS, Erlich HA, Higuchi R (1992) Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl 1:241–250
Ward AJ, Cooper TA (2010) The pathobiology of splicing. J Pathol 220:152–163
Yang M, Wu J, Wu SH et al (2012) Splicing of mouse p53 pre-mRNA does not always follow the “first come, first served” principle and may be influenced by cisplatin treatment and serum starvation. Mol Biol Rep 39:9247–9256
Young CS, Pyle AD (2016) Exon skipping therapy. Cell 167:1144
Zeitlin S, Efstratiadis A (1984) In vivo splicing products of the rabbit β-globin pre-mRNA. Cell 39:589–602
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this chapter
Cite this chapter
Ham, K.A., Wilton, S.D., Aung-Htut, M.T. (2022). Nonsequential Pre-mRNA Splicing: From Basic Understanding to Impacts on Splice-Manipulating Therapies. In: Jurga, S., Barciszewski, J. (eds) Messenger RNA Therapeutics. RNA Technologies, vol 13. Springer, Cham. https://doi.org/10.1007/978-3-031-08415-7_19
Download citation
DOI: https://doi.org/10.1007/978-3-031-08415-7_19
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-08414-0
Online ISBN: 978-3-031-08415-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)