- Open Access
Splicing regulators: targets and drugs
© BioMed Central Ltd 2005
- Published: 1 December 2005
Silencing of splicing regulators by RNA interference, combined with splicing-specific microarrays, has revealed a complex network of distinct alternative splicing events in Drosophila, while a high-throughput screen of more than 6,000 compounds has identified drugs that interfere specifically and directly with one class of splicing regulators in human cells.
- Spinal Muscular Atrophy
- Alternative Splice Event
- Indole Derivative
- Splice Regulator
- Exonic Splice Enhancer
The importance of splicing in the control of gene expression is underscored by the realization that the human genome codes for far fewer genes than expected : we do not have many more genes than the nematode Caenorhabditis elegans and have fewer than the plant Arabidopsis thaliana. Alternative splicing, whereby regulated splice-site usage results in the generation of different protein isoforms for the same gene locus, is key to multiplying the diversity of proteins produced from the human transcriptome. Computational alignments of transcript data and high-throughput splicing-specific microarray analyses have estimated that as many as 70% of human genes undergo alternative splicing [2, 3].
Complete genome sequences and microarray technology have made possible the large-scale study of splicing and the detection of alternatively spliced exons [2, 15, 16], but there is still much to do to uncover the 'splicing code'. This will involve identifying the cis-acting elements in exons and introns, identifying the regulators they bind, and understanding their mode of action in different cell types and at various developmental stages. Associations between regulators and splicing events have traditionally been made by biochemical and genetic methods. Although valuable, these methods are slow and can only study one regulator or one splicing event at a time. At present, a complete 'mapping' between regulators and their target exons via cis-regulatory elements is not yet available for any species. Such a map will be important in revealing the mechanisms involved in context-dependent inclusion and exclusion of alternative exons (as in different cell types or developmental stages), as well as in the design of low-toxicity drugs to alter splicing in the correction of genetic disorders or to disrupt viral gene expression. Two recent publications exemplify high-throughput and systematic strategies: Blanchette and colleagues  tackled the identification of targets of four splicing regulators in Drosophila melanogaster with a splicing-sensitive microarray, while Soret et al.  screened for chemical compounds that directly bind to SR proteins in human cells and interfere with spliceosomal assembly. The application of these methods to the study of more regulators and more compounds will pave the way for future attempts to develop therapies for diseases arising from aberrant splicing.
In order to identify the alternative splicing events controlled by specific splicing regulators, Blanchette et al.  made use of a recent experimental innovation - the combination of the silencing of regulators with splicing-sensitive microarrays to detect the effects. This technology has the potential not only rapidly to identify the targets of these regulators throughout the genome, but also to tease apart their combinatorial control. Blanchette et al.  investigated four well-characterized and highly expressed splicing regulators - the SR proteins dASF (Drosophila alternative splicing factor, the homolog of human ASF, also known as splicing factor 2; SF2) and B52 (the Drosophila equivalent of the mammalian SRp55 protein) and the hnRNPs PSI and hrp48. They developed a splicing-sensitive microarray platform to monitor around 3,000 annotated alternatively spliced genes in the Drosophila genome. As in other studies [2, 15, 19], oligonucleotide probes were designed to span annotated alternatively spliced junctions, with control probes across the relevant constitutive junctions (that is, junctions that are always spliced together) and within exons. In order to silence the regulators by RNA interference (RNAi), Drosophila SL2 cells were treated with double-stranded RNAs specific for each regulator gene. As these regulators are likely to be associated not only with splicing but also with other RNA-processing functions, Blanchette et al.  initially feared that a decrease in the levels of the regulators might affect pre-mRNA processing in such a general manner that the array data would be uninterpretable. Fortunately, hierarchical clustering of multiple RNAi experiments showed characteristic and reproducible splicing responses.
The RNA isolated from the siRNA-treated cells was then hybridized on the microarrays. Each regulator affected distinct sets of splice junctions, but the results revealed significant overlap in the targets of dASF/SF2 and B52/SRp55, consistent with the observation that SR proteins can complement one another on particular targets (see references cited in ). The authors also observed that almost all the events affected by PSI are also controlled by hrp48, suggesting that hrp48 is a required partner for PSI. Interestingly, this relationship does not seem to be mutual, but further experiments are necessary to confirm this finding. Figure 1 illustrates this scenario: regulator II is an obligatory partner to I, but I is not required for II.
Consistent with the notion that dASF/SF2 is a general regulator of alternative splicing, its knockdown affected the largest number of events (319 events). Conversely, PSI, a more specific regulator of alternative splicing, affected the fewest events (43 events). In order to obtain evidence for direct binding of B52/SRp55, a positional weight matrix of an identified binding site for B52/SRp55 was used to scan the exon-intron boundaries of splicing events affected by knockdown of the factor. The motif was indeed specifically over-represented at the 5' splice sites of exons at which splicing is reduced when B52/SRp55 is knocked down. Together, the findings revealed a network of tens to hundreds of alternative splicing events that are regulated by individual or combinations of splicing regulators.
As acknowledged by Blanchette et al. , questions still remain about why some targets are affected similarly by different regulators. There might be co-occurring binding sites in the same set of exons, or the regulators might have overlapping binding specificities, or the regulators might be interacting with another common regulator already present. Knockdowns and overexpression of more splicing factors, and parallel analyses of the sequence similarity of regulated exons (and flanking introns), as well as the RNA binding domain characteristics of the splicing regulators, should clarify these questions.
Various ways of correcting splicing defects have been sought. Disease-associated exons can be induced to skip by antisense oligonucleotides [20, 21], or exon inclusion can be restored by synthetic exon-specific effectors  or mediated by RNA trans-splicing . Although they are effective in correcting the splicing defect, these methods are not readily adaptable to high-throughput analysis with a view to finding drugs that rescue aberrant splicing events.
To determine which stage of spliceosome assembly was affected, Soret et al.  then added 32P-labeled βglo-3S pre-mRNA to HeLa nuclear extracts and incubated the mixture with each of the three compounds. An early step of assembly must have been disrupted, as no splicing complexes were formed. Realizing that monitoring spliceosome assembly would be a more straightforward way of identifying compounds that affect splicing, the authors screened 1,500 small molecules and identified 25 candidates (Figure 2b). Surprisingly, these all have similar structures, being indole derivatives of the pyridocarbazole, benzopyridoindole or pyrido-pyrrolo-isoquinoline classes.
As icing on the cake, Soret et al.  looked at the effects of their indole derivatives on the splicing of the pre-mRNA of the human immunodeficiency virus HIV-1. This pre-mRNA is regulated by alternative splicing involving SR proteins such as ASF/SF2 and SC35. Chronically infected human promonocytic U1 cell lines, which can be stimulated to produce large quantities of HIV-1 pre-mRNA, were treated with a number of indole derivatives . Several of these were shown specifically to affect HIV-1 alternative splicing, and abolished HIV-1 virion production. Neither cell viability nor the splicing profiles of endogenous genes were affected, indicating the potentially low toxicity of this treatment. This remarkable discovery opens new approaches to treatment of HIV-1 infection by indole derivatives via the interruption of ESE-mediated alternative splicing.
The studies of Blanchette et al.  and Soret et al.  are the first large-scale screens for the genome-wide targets of a small set of splicing regulators and for compounds that disrupt a specific class of splicing regulators. One can envisage combining the power of the two methods. For example, splicing-specific microarrays can query alternative splicing events affected by particular compounds. Comparing these events to alternative events affected by knockdowns of particular regulators may identify the candidate regulators affected by the compounds. More comprehensive siRNA screens of other RNA-binding proteins  using splicing-specific microarrays could point to new roles for splicing modulation. Looking forward, a large-scale mapping of regulators to targets in humans, and of compounds to regulators, combined with computational extraction of potential cis-regulatory binding sites, will be essential in the screening and correction of splicing defects in human disease.
G.Y. is supported by the Crick-Jacobs fellowship at the Salk Institute. G.Y. acknowledges Xiang-dong Xu and Nicole Coufal for helpful comments on the manuscript.
- Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062.PubMedView ArticleGoogle Scholar
- Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD: Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science. 2003, 302: 2141-2144. 10.1126/science.1090100.PubMedView ArticleGoogle Scholar
- Modrek B, Resch A, Grasso C, Lee C: Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 2001, 29: 2850-2859. 10.1093/nar/29.13.2850.PubMedPubMed CentralView ArticleGoogle Scholar
- Ladd AN, Cooper TA: Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol. 2002, 3: reviews0008.1-0008.16. 10.1186/gb-2002-3-11-reviews0008.View ArticleGoogle Scholar
- Zheng ZM: Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. J Biomed Sci. 2004, 11: 278-294.PubMedPubMed CentralView ArticleGoogle Scholar
- Graveley BR: Sorting out the complexity of SR protein functions. RNA. 2000, 6: 1197-1211. 10.1017/S1355838200000960.PubMedPubMed CentralView ArticleGoogle Scholar
- Del Gatto-Konczak F, Olive M, Gesnel MC, Breathnach R: hnRNP A1 recruited to an exon in vivo can function as an exon splicing silencer. Mol Cell Biol. 1999, 19: 251-260.PubMedPubMed CentralView ArticleGoogle Scholar
- Zhu J, Mayeda A, Krainer AR: Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. Mol Cell. 2001, 8: 1351-1361. 10.1016/S1097-2765(01)00409-9.PubMedView ArticleGoogle Scholar
- Caceres JF, Stamm S, Helfman DM, Krainer AR: Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science. 1994, 265: 1706-1709.PubMedView ArticleGoogle Scholar
- Musunuru K: Cell-specific RNA-binding proteins in human disease. Trends Cardiovasc Med. 2003, 13: 188-195. 10.1016/S1050-1738(03)00075-6.PubMedView ArticleGoogle Scholar
- Faustino NA, Cooper TA: Pre-mRNA splicing and human disease. Genes Dev. 2003, 17: 419-437. 10.1101/gad.1048803.PubMedView ArticleGoogle Scholar
- Cartegni L, Chew SL, Krainer AR: Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet. 2002, 3: 285-298. 10.1038/nrg775.PubMedView ArticleGoogle Scholar
- Caceres JF, Kornblihtt AR: Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. 2002, 18: 186-193. 10.1016/S0168-9525(01)02626-9.PubMedView ArticleGoogle Scholar
- Garcia-Blanco MA, Baraniak AP, Lasda EL: Alternative splicing in disease and therapy. Nat Biotechnol. 2004, 22: 535-546. 10.1038/nbt964.PubMedView ArticleGoogle Scholar
- Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, et al: Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell. 2004, 16: 929-941. 10.1016/j.molcel.2004.12.004.PubMedView ArticleGoogle Scholar
- Clark TA, Sugnet CW, Ares M: Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science. 2002, 296: 907-910. 10.1126/science.1069415.PubMedView ArticleGoogle Scholar
- Blanchette M, Green RE, Brenner SE, Rio DC: Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev. 2005, 19: 1306-1314. 10.1101/gad.1314205.PubMedPubMed CentralView ArticleGoogle Scholar
- Soret J, Bakkour N, Maire S, Durand S, Zekri L, Gabut M, Fic W, Divita G, Rivalle C, Dauzonne D, et al: Selective modification of alternative splicing by indole derivatives that target serine-arginine-rich protein splicing factors. Proc Natl Acad Sci USA. 2005, 102: 8764-8769. 10.1073/pnas.0409829102.PubMedPubMed CentralView ArticleGoogle Scholar
- Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM: Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol. 2003, 4: R66-10.1186/gb-2003-4-10-r66.PubMedPubMed CentralView ArticleGoogle Scholar
- Skordis LA, Dunckley MG, Yue B, Eperon IC, Muntoni F: Bifunctional antisense oligonucleotides provide a trans-acting splicing enhancer that stimulates SMN2 gene expression in patient fibroblasts. Proc Natl Acad Sci USA. 2003, 100: 4114-4119. 10.1073/pnas.0633863100.PubMedPubMed CentralView ArticleGoogle Scholar
- Dunckley MG, Manoharan M, Villiet P, Eperon IC, Dickson G: Modification of splicing in the dystrophin gene in cultured Mdx muscle cells by antisense oligoribonucleotides. Hum Mol Genet. 1998, 7: 1083-1090. 10.1093/hmg/7.7.1083.PubMedView ArticleGoogle Scholar
- Cartegni L, Krainer AR: Correction of disease-associated exon skipping by synthetic exon-specific activators. Nat Struct Biol. 2003, 10: 120-125. 10.1038/nsb887.PubMedView ArticleGoogle Scholar
- Garcia-Blanco MA: Messenger RNA reprogramming by spliceosome-mediated RNA trans-splicing. J Clin Invest. 2003, 112: 474-480. 10.1172/JCI200319462.PubMedPubMed CentralView ArticleGoogle Scholar
- Park JW, Parisky K, Celotto AM, Reenan RA, Graveley BR: Identification of alternative splicing regulators by RNA interference in Drosophila. Proc Natl Acad Sci USA. 2004, 101: 15974-15979. 10.1073/pnas.0407004101.PubMedPubMed CentralView ArticleGoogle Scholar