Substances that change alternative splice site selection

The recognition of alternative exons is frequently subjected to regulation. The utilisation of an alternative exon depends on the cell type, the developmental stage, and/or the reception of cellular signals [reviewed in (Blaustein et al., 2007; Shin and Manley, 2004; Stamm, 2002)]. These changes can occur within one hour in animal systems (Daoud et al., 1999), and in most systems studied, these changes do not involve de novo protein synthesis (Stamm, 2002). Post-translational modifications of splicing factors, such as phosphorylation [reviewed in (Stamm, 2008)], glycosylation (Soulard et al., 1993), acetylation (Babic et al., 2004), or methylation (Rho et al., 2007), also play key roles in the regulation of splice-site selection.

The importance of proper splice site recognition is apparent from the growing number of human diseases that are recognised to be caused by the selection of incorrect splice sites (Faustino and Cooper, 2003; Stoilov et al., 2002). These diseases result from either mutations, as in the case of FTDP-17 and Duchenne’s Muscular Dystrophy or deregulation of the cellular splicing machinery, as exemplified by the numerous changes in alternative splicing seen in cancer (Venables, 2006). Alternative splicing has therefore rapidly emerged as a new drug target (Hagiwara, 2005), especially since protein isoforms generated by this process can have different pharmacological effects (Bracco and Kearsey, 2003). The unexpected alteration of alternative splice site selection may also explain side-effects that established drugs have in addition to their principal role.

EURASNET groups (for example, Stefan Stamm, Jamal Tazi, Angus Lamond) are involved in the discovery of substances which can alter alternative splicing.

The use of RNA-binding molecules as antibiotics, such as gentamicin, chloramphenicol, and tetracycline illustrates that drugs can be targeted against RNA and/or RNA binding proteins. High-throughput screens and testing of substances in model systems identified more substances that change splice site selection. The substances fall into several categories, including HDAC inhibitors, kinase and phosphatase inhibitors, as well as cAMP antagonist and agonists. The currently known substances are reviewed in (Sumanasekera et al., 2008 (in press)) and updated on this page.

If you find a substance that is not listed here or if you are looking for a reporter gene to study such substances, please contact Chiranthani Sumanasekera.

	Small Molecule Name	Mechanism	Regulated Exon	Structure	Reference
Histone Deacetylase (HDAC) Inhibitors
1	sodium butyrate	HDAC inhibitor	SMN2 exon 7
2	valproic acid	HDAC inhibitor	SMN2 exon 7
3	sodium 4-phenylbutyrate	HDAC inhibitor	SMN2 exon 7
4	N-hydroxyl-7-(4- (dimethylamino)benzoyl) aminoheptanamide (M344)	HDAC inhibitor	SMN2 exon 7
5	suberoylanilide hydroxamic acid (SAHA)	HDAC inhibitor	SMN2 exon 7
Kinase Inhibitors
6	aclarubicin	Topo I	SMN2 exon 7
7	camptothecin	Topo I	CASP-2 exon 9
8	6-N-formylamino-12,13- dihydro-1,11-dihydroxy-13- (β-D-glucopyranosyl) 5H-indolo  [2,3-a]pyrrolo [3,4-c]carbazole-5,7 (6H)-dione (NB-506)	Topo I	Bcl-X  and CD 44
9	isodiospyrin	Topo I	Not defined (ND)
10	(Z)-1-(3-ethyl-5-methoxy-2, 3-dihydrobenzothiazol- 2-ylidene) propan-2-one (TG003)	CLK kinases	Clk1/sty exon 2 and E1A
11	lithium chloride	GSK3	Tau exon 10	LiC1
12	N-(4-methoxybenzyl)-N’- (5-nitro-1,3-thiazol-2-yl) urea (AR-A014418)	GSK3	Tau  exon 10
Phosphatase Inhibitors
13	sodium orthovanadate	non-specific inhibitor	SMN2 exon 7	Na3VO4
14	N-(hexanoyl)sphingosine (C6-ceramide)	PP1 regulation	Bcl-X and  CASP-9
15	tautomycin	PP1 inhibition	SMN2 exon 7 and multiple other exons
16	cantharidin	PP1 inhibition	SMN2       exon 7
cAMP Pathway
17	rac-2-[4-(1-oxo-2- isoindolinyl) phenyl]propionic acid (indoprofen)	phospho-diesterase inhibitor?	SMN2
18	2-(tert-butylamino)-1- (4-hydroxy-3- hydroxymethylphenyl) ethanol sulfate (salbutamol)	adrenergic antagonist	SMN2 exon 7
SR-Protein-Protein Interactions
19	10-chloro-2,6- dimethyl-2H- pyrido[3’,4’:4,5] pyrrolo[2,3-g]isoquinoline (IDC16)	SR-protein interaction	HIV-1 mRNA
Coupling of Transcription and Splicing
20	dexamethazone coupling of transcription and splicing	coupling of transcription and spclicing	Insulin receptor mRNA
21	dihydroepiandrosterone (DHEA)	coupling of transcription and splicing	Stress axis-regulated (STREX) exon
22	steroid hormones	ND	Reporter CD44 mini-gene
Ion Channels and Electrochemical Gradients
23	5-(N-ethyl-N-isopropyl) amiloride (EIPA)	change in ion gradient	SMN2
24	glutamate	change in ion gradient	Ania-6 mRNA
Unknown Role
25	hydroxyurea	ND	SMN2 exon 7
26	ethanol	ND	L-type Ca2+ channel mRNA
27	dimethyl sulfoxide (DMSO)	ionic interaction
28	6-furfuryladenine (kinetin)	ND	IKBKAP mRNA
29	etoposide (VP16)	Topo II inhibition?	CASP-2 exon 9
30	epigallocatechin gallate (EGCG)	down-regulate the expression of hnRNP A2/B1	SMN2 exon 7 IKBKAP mRNA
31	cucurmin	ND	SMN2 exon 7
32	resveratrol	ND	SMN2 exon 7