Alternative pre-mRNA splicing is an important element in eukaryotic gene expression, as most of the protein-coding genes use this process to generate multiple protein isoforms from a single gene. An increasing number of human diseases are now recognized to be caused by the selection of ‘wrong’ alternative exons. Research during the last few years identified a number of low–molecular-mass chemical substances that can change alternative exon usage. Most of these substances act by either blocking histone deacetylases or by interfering with the phosphorylation of splicing factors. How the remaining large number of these substances affect splicing is not yet fully understood. The emergence of these low-molecular-mass substances provides not only probes for studying alternative pre-mRNA splicing, but also opens the door to the possible harnessing of these compounds as drugs to control diseases caused by the selection of ‘wrong’ splice sites.

Importance of alternative splicing

Most of the human protein-coding genes exhibit an exon–intron structure that becomes apparent when their pre-mRNA is processed. During pre-mRNA processing, some sequences are joined and exported into the cytosol as exons (for exported sequences). The introns (intervening sequences) are excised and retained in the nucleus.

In humans, almost all polymerase II transcripts are spliced, and an estimated 74–88% of human genes are alternatively spliced [1,2]. Most of the alternative exons encode portions of proteins, and therefore alternative splicing facilitates the generation of multiple protein isoforms from a single gene. These isoforms often have different biological properties in that they interact with other binding partners and possess different subcellular localizations, catalytic activities or pharmacological properties [3]. Several biological processes are co-ordinated by orchestrated changes in alternative splicing. Well-studied examples of these processes include sex determination in Drosophila [4] and certain apoptotic events [5]. The potential of alternative pre-mRNA splicing to increase the number of proteins generated from a single gene demonstrates that alternative pre-mRNA splicing is a central element of eukaryotic gene regulation and explains why it has been selected during evolution.

The recognition of exons in the pre-mRNA is a dynamic process that is coupled with transcription and other pre-mRNA processing steps, such as 5′-end capping, 3′-end processing, polyadenylation and editing. Since the sequences of the splice sites that surround exons are highly degenerate, additional sequences on the pre-mRNA aid in exon recognition. The interplay between these sequences on the pre-mRNA and more than 300 proteins (reviewed in [6]) that have been identified in MS analyses leads ultimately to the recognition of the splice sites by the spliceosome and the joining of exons [7].

The recognition of alternative exons is frequently subjected to regulation. The utilization of an alternative exon depends on the cell type, the developmental stage and/or the reception of cellular signals (reviewed in [810]). These changes can occur within 1 h in animal systems [11], and in most systems studied, these changes do not involve de novo protein synthesis [8]. Post-translational modifications of splicing factors, such as phosphorylation (reviewed in [12]), glycosylation [13], acetylation [14] or methylation [15], 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 recognized to be caused by the selection of incorrect splice sites [16,17]. These diseases result from either mutations, as in the case of FTDP-17 (frontotemporal dementia and parkinsonism linked to chromosome 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 [18]. Alternative splicing has therefore rapidly emerged as a new drug target [19], especially since protein isoforms generated by this process can have different pharmacological effects [20]. The unexpected alteration of alternative splice-site selection may also explain the side effects that established drugs have in addition to their principal role.

Given the importance of alternative splicing, it is surprising that no low-molecular-mass compounds have been identified that specifically inhibit certain splicing events or stages in the splicing reaction. The use of RNA-binding molecules as antibiotics, such as gentamicin, chloramphenicol and tetracycline, certainly illustrates that drugs can be targeted against RNA and/or RNA-binding proteins.

The lack of compounds for the activation or inhibition of specific pre-mRNA splicing events is a problem for studying the splicing reaction itself and for the generation of therapeutic approaches to treat diseases caused by missplicing. During the last 5 years, research focused on changing incorrect splice-site selection to the desired outcome led to the identification of several low-molecular-mass components, which are the subject of the present review. So far, the common feature of these compounds is the low degree of specificity with which they affect numerous splicing events.

Several of these components, such as lithium chloride or valproic acid, are in clinical use to treat bipolar disorders or epilepsy respectively. They were only recently shown to influence splice-site selection [21,22]. It is possible that other pharmaceuticals now in clinical use also affect pre-mRNA splicing. Currently, only the use of oligonucleotides allows the unambiguous, specific targeting of a splicing event. This technique is currently being tested for Duchenne's muscular dystrophy and is in the experimental stage for other diseases, such as SMA (spinal muscular atrophy) and thalassemia (reviewed in [23,24]).

Substances regulating splice-site selection

Several screens have been performed to find substances that might change the missplicing that is the cause of SMA or that could be a basis for HIV therapy. In addition, a number of individual investigations discovered several substances capable of changing splice-site selection, which are summarized in Table 1.

Table 1
Names, putative mechanisms, regulated exons and structures of the low-molecular-mass substances that influence alternative splice-site selection

Abbreviation: n.d., not defined.

No.Small molecule nameMechanismRegulated exonStructureReference
 HDAC inhibitors     
 Sodium butyrate HDAC inhibitor SMN2 exon 7 CH3(CH2)2CO2Na [26
 Valproic acid HDAC inhibitor SMN2 exon 7 (CH3CH2CH2)2CHCO2[22
 Sodium 4-phenylbutyrate HDAC inhibitor SMN2 exon 7 C6H5(CH2)3CO2Na [41
N-Hydroxyl-7-[4-(dimethylamino)benzoyl]aminoheptanamide (M344) HDAC inhibitor SMN2 exon 7 
graphic
 
[42
 SAHA HDAC inhibitor SMN2 exon 7 
graphic
 
[43
 Kinase inhibitors     
 Aclarubicin Topo I SMN2 exon 7 
graphic
 
[44
 Camptothecin Topo I CASP-2 exon 9 
graphic
 
[45
 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 CD44 
graphic
 
[46
 Isodiospyrin Topo I n.d. 
graphic
 
[47
10  (Z)-1-(3-Ethyl-5-methoxy-2,3-dihydrobenzothiazol-2-ylidene) propan-2-one (TG003) CLK kinases Clk1/sty exon 2 and E1A 
graphic
 
[29
11  Lithium chloride GSK3 tau exon 10 LiCl [21
12 N-(4-Methoxybenzyl)-N′-(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418) GSK3 tau exon 10 
graphic
 
[21,48
 Phosphatase inhibitors     
13  Sodium orthovanadate Non-specific inhibitor SMN2 exon 7 Na3VO4 [49
14 N-(Hexanoyl)sphingosine (C6-ceramide) PP1 regulation Bcl-X and CASP-9 
graphic
 
[33
15  Tautomycin PP1 inhibition SMN2 exon 7 and multiple other exons 
graphic
 
[32
16  Cantharidin PP1 inhibition SMN2 exon 7 
graphic
 
[32
 cAMP pathway     
17 rac-2-[4-(1-Oxo-2-isoindolinyl)phenyl]propionic acid (indoprofen) Phosphodiesterase inhibitor? SMN2 
graphic
 
[35
18  2-(t-Butylamino)-1-(4-hydroxy-3-hydroxymethylphenyl)ethanol sulfate (salbutamol) Adrenergic antagonist SMN2 exon 7 
graphic
 
[34
 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 
graphic
 
[38,39
 Coupling of transcription and splicing     
20  Dexamethasone Coupling of transcription and splicing Insulin receptor mRNA 
graphic
 
[50
21  DHEA (dihydroepiandrosterone) Coupling of transcription and splicing STREX (stress axis-regulated) exon 
graphic
 
[51
22  Steroid hormones n.d. Reporter CD44 mini-gene  [35
 Ion channels and electrochemical gradients     
23  EIPA Change in ion gradient SMN2 
graphic
 
[52
24  Glutamate Change in ion gradient Ania-6 mRNA C5H9NO4 [53,54
 Unknown role     
25  Hydroxyurea n.d. SMN2 exon 7 
graphic
 
[55
26  Ethanol n.d. L-type Ca2+ channel mRNA C2H5OH [56
27  DMSO Ionic interaction Multiple 
graphic
 
[57
28  6-Furfuryladenine (kinetin) n.d. IKBKAP mRNA 
graphic
 
[58
29  Etoposide (VP16) Topo II inhibition? CASP-2 exon 9 
graphic
 
[59
30  EGCG (epigallocatechin gallate) Down-regulates the expression of hnRNP A2/B1 SMN2 exon 7, IKBKAP mRNA 
graphic
 
[60,61
31  Cucurmin n.d. SMN2 exon 7 
graphic
 
[60
32  Resveratrol n.d. SMN2 exon 7 
graphic
 
[60
No.Small molecule nameMechanismRegulated exonStructureReference
 HDAC inhibitors     
 Sodium butyrate HDAC inhibitor SMN2 exon 7 CH3(CH2)2CO2Na [26
 Valproic acid HDAC inhibitor SMN2 exon 7 (CH3CH2CH2)2CHCO2[22
 Sodium 4-phenylbutyrate HDAC inhibitor SMN2 exon 7 C6H5(CH2)3CO2Na [41
N-Hydroxyl-7-[4-(dimethylamino)benzoyl]aminoheptanamide (M344) HDAC inhibitor SMN2 exon 7 
graphic
 
[42
 SAHA HDAC inhibitor SMN2 exon 7 
graphic
 
[43
 Kinase inhibitors     
 Aclarubicin Topo I SMN2 exon 7 
graphic
 
[44
 Camptothecin Topo I CASP-2 exon 9 
graphic
 
[45
 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 CD44 
graphic
 
[46
 Isodiospyrin Topo I n.d. 
graphic
 
[47
10  (Z)-1-(3-Ethyl-5-methoxy-2,3-dihydrobenzothiazol-2-ylidene) propan-2-one (TG003) CLK kinases Clk1/sty exon 2 and E1A 
graphic
 
[29
11  Lithium chloride GSK3 tau exon 10 LiCl [21
12 N-(4-Methoxybenzyl)-N′-(5-nitro-1,3-thiazol-2-yl)urea (AR-A014418) GSK3 tau exon 10 
graphic
 
[21,48
 Phosphatase inhibitors     
13  Sodium orthovanadate Non-specific inhibitor SMN2 exon 7 Na3VO4 [49
14 N-(Hexanoyl)sphingosine (C6-ceramide) PP1 regulation Bcl-X and CASP-9 
graphic
 
[33
15  Tautomycin PP1 inhibition SMN2 exon 7 and multiple other exons 
graphic
 
[32
16  Cantharidin PP1 inhibition SMN2 exon 7 
graphic
 
[32
 cAMP pathway     
17 rac-2-[4-(1-Oxo-2-isoindolinyl)phenyl]propionic acid (indoprofen) Phosphodiesterase inhibitor? SMN2 
graphic
 
[35
18  2-(t-Butylamino)-1-(4-hydroxy-3-hydroxymethylphenyl)ethanol sulfate (salbutamol) Adrenergic antagonist SMN2 exon 7 
graphic
 
[34
 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 
graphic
 
[38,39
 Coupling of transcription and splicing     
20  Dexamethasone Coupling of transcription and splicing Insulin receptor mRNA 
graphic
 
[50
21  DHEA (dihydroepiandrosterone) Coupling of transcription and splicing STREX (stress axis-regulated) exon 
graphic
 
[51
22  Steroid hormones n.d. Reporter CD44 mini-gene  [35
 Ion channels and electrochemical gradients     
23  EIPA Change in ion gradient SMN2 
graphic
 
[52
24  Glutamate Change in ion gradient Ania-6 mRNA C5H9NO4 [53,54
 Unknown role     
25  Hydroxyurea n.d. SMN2 exon 7 
graphic
 
[55
26  Ethanol n.d. L-type Ca2+ channel mRNA C2H5OH [56
27  DMSO Ionic interaction Multiple 
graphic
 
[57
28  6-Furfuryladenine (kinetin) n.d. IKBKAP mRNA 
graphic
 
[58
29  Etoposide (VP16) Topo II inhibition? CASP-2 exon 9 
graphic
 
[59
30  EGCG (epigallocatechin gallate) Down-regulates the expression of hnRNP A2/B1 SMN2 exon 7, IKBKAP mRNA 
graphic
 
[60,61
31  Cucurmin n.d. SMN2 exon 7 
graphic
 
[60
32  Resveratrol n.d. SMN2 exon 7 
graphic
 
[60

HDAC (histone deacetylase) inhibitors

HDAC inhibitors were identified in studies aimed at augmenting the usage of SMN2 (survival of motor neurons 2) exon 7, an outcome that would be a therapeutically valuable approach in the treatment of SMA. These inhibitors include sodium butyrate, valproic acid, sodium 4-phenylbutyrate, M344 and SAHA (suberoylanilide hydroxamic acid) (Table 1, numbers 1–5). In mouse models of SMA, these compounds increased the life span of the animals (reviewed in [25]). Their mechanism of action, however, is not yet clear. Among possible explanations is the role of HDACs. HDACs regulate the chromatin structure and subsequently gene expression by controlling the acetylation state of histones, which in turn determines histone affinity for DNA. It is possible that application of HDAC inhibitors causes a co-ordinated change in the expression of splicing regulatory factors, which in turn dictates a change in splicing. In support of this hypothesis, a change in SR protein (serine/arginine-rich protein) expression was observed after sodium butyrate application in mice [26]. Another possibility, which has not been systematically investigated, is a direct effect of these substances on the acetylation of splicing-regulatory proteins themselves. Acetylation of SAM68 (68 kDa Src-associated protein in mitosis), for example, regulates its binding to RNA [14], and it is possible that other splicing factors are regulated similarly.

Substances that change the phosphorylation state of splicing-regulatory proteins

As mentioned above, reversible phosphorylation is an important mechanism in controlling the selection of alternative exons. As a consequence, kinase and phosphatase inhibitors also affect alternative splice-site selection. The best understood targets for kinases acting on splicing are the SR proteins, a family of highly conserved pre-mRNA splicing factors. SR proteins can bind to each other and the SR domain serves mainly as a protein–protein interaction domain, allowing different SR proteins to oligomerize. This oligomerization is the basis for the formation of exon enhancer complexes. In addition, the SR domain can bind to RNA. It has been shown in several systems that the phosphorylation state of this domain controls the oligomerization of SR proteins that is the basis for the formation of exon-recognition complexes. The phosphorylation state of the SR domain is controlled by the interplay of multiple kinases and phosphatases, located both in the cytosol and the nucleoplasm [12].

Kinase inhibitors

DNA Topo I (topoisomerase I) effects the phosphorylation of SR proteins [27] and has a dual function in RNA metabolism. It nicks the DNA strand upon transcription, and phosphorylates SR proteins that are known to associate with the nascent pre-mRNA [28]. Numerous antineoplastic drugs that target Topo I were tested for their effect on splice-site selection, and several of them (Table 1, numbers 6–9) changed splice-site selection.

SR proteins are also phosphorylated by a family of nuclear CDC2 (cell division cycle 2 kinase)-related kinases, termed CLK (CDC-like kinase) 1–4. A specific inhibitor against these kinases, TG003 (Table 1, number 10), changes alternative splicing in reporter genes [29] and has been tested as an antiviral agent [30]. GSK3 (glycogen synthase kinase 3) also phosphorylates SR proteins, and its inhibition changes alterative splicing of exon 10 of the tau gene [21] (Table 1, numbers 11 and 12). This exon is of medical importance, as mutations causing aberrant usage of the exon leads to frontotemporal dementia (FTDP-17) [31].

Phosphatase inhibitors

PP1 (protein phosphatase-1) binds directly to a phylogenetically conserved motif in the RNA-recognition motif of at least nine different splicing-regulatory proteins [32]. As a consequence, blocking PP1 activity has a strong influence on alternative splicing. The most specific inhibitor for PP1 is tautomycin, which changes alternative splicing in cell culture and mouse models [32]. Similar effects were seen for cantharidin, which inhibits both PP1 and PP2A (protein phosphatase-2A) (Table 1, numbers 13–16). Ceramides activate PP1 by an unknown mechanism that probably involves dissociation of the phosphatase from its inhibitors. C6-ceramide, shown in Table 1 [14], has been shown to change splice-site selection in some apoptotic genes. The change in alternative splicing of genes involved in apoptosis explains the cytotoxic effect of these drugs that are used in chemotherapy [33].

In vivo, PP1 is blocked by specific protein inhibitors, Inhibitor-1 and DARPP-32 (dopamine- and cAMP-regulated phosphoprotein of 32 kDa), which are activated by phosphorylation by PKA (protein kinase A). Since PKA is activated by a rise in cellular cAMP levels, cAMP increase leads to a decrease in PP1 activity, which has an effect on splice-site selection. This mechanistic link explains the actions of salbutamol [34] (a β2-adrenergic agonist) and indoprofen [35] (a compound that blocks cyclo-oxygenase and phosphodiesterase) on splicing (Table 1, numbers 17 and 18).

Steroid hormones

The selection of alternative exons is coupled with promoter usage, as the C-terminal domain of polymerase II interacts with components of the splicing machinery. This outcome explains why alternative splicing events can be controlled by steroid hormones when their pre-mRNA transcription is controlled by steroid-responsive promoters [36]. In addition, CAPER [co-activator of AP-1 (activator protein-1) and ER (oestrogen receptor)] proteins have been identified that are activated by steroid hormones and act on both transcription and splicing [37] (Table 1, numbers 20 and 21).

Protein–protein interaction

The interaction between SR proteins can be interrupted by isoquinolines, which target specific members of this class of proteins. These findings can be applied in vitro to block HIV replication [38,39] (Table 1, number 19).

Ion channels

Alternative splicing events change in response to neuronal stimulation [11,40]. Several compounds, including valproic acid, glutamate and EIPA [5-(N-ethyl)-N-isopropylamiloride], affect splicing in cell culture. However, the exact mechanism that links this change in membrane properties to the splicing machinery remains unclear (Table 1, numbers 23 and 24).

Other components

Still other investigations identified a group of apparently unrelated compounds that affect alternative splicing. The mechanism of action of these compounds remains unclear (Table 1, numbers 25–32).

Future developments

The compounds in Table 1 clearly underscore the dramatic ability of small molecules to affect alternative splicing decisions. Their discovery raises the prospect for finding still other natural, synthetic or semi-synthetic compounds that will directly interact with the spliceosome components or will indirectly alter signal transduction pathways that regulate splice-site selection. Finding substances that possess specificity for a single splicing event or for a certain step in the splicing process represents a future challenge that, once solved, will allow us to understand the fundamental aspects of this intriguing process and to treat human diseases caused by missplicing events.

RNA UK 2008: Independent Meeting held at The Burnside Hotel, Bowness on Windermere, Cumbria, U.K., 18–20 January 2008. Organized and Edited by David Elliot (Newcastle, U.K.), Sarah Newbury (Sussex, U.K.) and Alison Tyson-Capper (Newcastle, U.K.).

Abbreviations

     
  • EIPA

    5-(N-ethyl)-N-isopropylamiloride

  •  
  • FTDP-17

    frontotemporal dementia and parkinsonism linked to chromosome 17

  •  
  • HDAC

    histone deacetylase

  •  
  • PKA

    protein kinase A

  •  
  • PP1

    protein phosphatase-1

  •  
  • SAHA

    suberoylanilide hydroxamic acid

  •  
  • SMA

    spinal muscular atrophy

  •  
  • SMN2

    survival of motor neurons 2

  •  
  • SR

    protein, serine/arginine-rich protein

  •  
  • Topo

    I, topoisomerase I

This work was supported by the EURASNET (European Alternative Splicing Network of Excellence), NIH (National Institutes of Health; P20 RR020171 from the National Center for Research Resources), BMBF (Federal Ministry of Education and Research, Germany), DFG (Deutsche Forschungsgemeinschaft; SFB 473) and the German Cancer Aid.

References

References
1
Kampa
 
D.
Cheng
 
J.
Kapranov
 
P.
Yamanaka
 
M.
Brubaker
 
S.
Cawley
 
S.
Drenkow
 
J.
Piccolboni
 
A.
Bekiranov
 
S.
Helt
 
G.
, et al 
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
Genome Res.
2004
, vol. 
14
 (pg. 
331
-
342
)
2
Johnson
 
J.M.
Castle
 
J.
Garrett-Engele
 
P.
Kan
 
Z.
Loerch
 
P.M.
Armour
 
C.D.
Santos
 
R.
Schadt
 
E.E.
Stoughton
 
R.
Shoemaker
 
D.D.
 
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
Science
2003
, vol. 
302
 (pg. 
2141
-
2144
)
3
Stamm
 
S.
Ben-Ari
 
S.
Rafalska
 
I.
Tang
 
Y.
Zhang
 
Z.
Toiber
 
D.
Thanaraj
 
T.A.
Soreq
 
H.
 
Function of alternative splicing
Gene
2005
, vol. 
344
 (pg. 
1
-
20
)
4
Forch
 
P.
Valcarcel
 
J.
 
Splicing regulation in Drosophila sex determination
Prog. Mol. Subcell. Biol.
2003
, vol. 
31
 (pg. 
127
-
151
)
5
Wu
 
J.Y.
Tang
 
H.
Havlioglu
 
N.
 
Alternative pre-mRNA splicing and regulation of programmed cell death
Prog. Mol. Subcell. Biol.
2003
, vol. 
31
 (pg. 
153
-
185
)
6
Jurica
 
M.S.
Moore
 
M.J.
 
Pre-mRNA splicing: awash in a sea of proteins
Mol. Cell
2003
, vol. 
12
 (pg. 
5
-
14
)
7
Smith
 
C.W.
Valcarcel
 
J.
 
Alternative pre-mRNA splicing: the logic of combinatorial control
Trends Biochem. Sci.
2000
, vol. 
25
 (pg. 
381
-
388
)
8
Stamm
 
S.
 
Signals and their transduction pathways regulating alternative splicing: a new dimension of the human genome
Hum. Mol. Genet.
2002
, vol. 
11
 (pg. 
2409
-
2416
)
9
Shin
 
C.
Manley
 
J.L.
 
Cell signalling and the control of pre-mRNA splicing
Nat. Rev. Mol. Cell Biol.
2004
, vol. 
5
 (pg. 
727
-
738
)
10
Blaustein
 
M.
Pelisch
 
F.
Srebrow
 
A.
 
Signals, pathways and splicing regulation
Int. J. Biochem. Cell Biol.
2007
, vol. 
39
 (pg. 
2031
-
2048
)
11
Daoud
 
R.
Da Penha Berzaghi
 
M.
Siedler
 
F.
Hubener
 
M.
Stamm
 
S.
 
Activity-dependent regulation of alternative splicing patterns in the rat brain
Eur. J. Neurosci.
1999
, vol. 
11
 (pg. 
788
-
802
)
12
Stamm
 
S.
 
Regulation of alternative splicing by reversible phosphorylation
J. Biol. Chem.
2008
, vol. 
283
 (pg. 
1223
-
1227
)
13
Soulard
 
M.
Della Valle
 
V.
Siomi
 
M.C.
Pinol-Roma
 
S.
Codogno
 
P.
Bauvy
 
C.
Bellini
 
M.
Lacroix
 
J.C.
Monod
 
G.
Dreyfuss
 
G.
Larsen
 
C.-J.
 
hnRNP G: sequence and characterization of a glycosylated RNA-binding protein
Nucleic Acids Res.
1993
, vol. 
21
 (pg. 
4210
-
4217
)
14
Babic
 
I.
Jakymiw
 
A.
Fujita
 
D.J.
 
The RNA binding protein Sam68 is acetylated in tumor cell lines, and its acetylation correlates with enhanced RNA binding activity
Oncogene
2004
, vol. 
23
 (pg. 
3781
-
3789
)
15
Rho
 
J.
Choi
 
S.
Jung
 
C.R.
Im
 
D.S.
 
Arginine methylation of Sam68 and SLM proteins negatively regulates their poly(U) RNA binding activity
Arch. Biochem. Biophys.
2007
, vol. 
466
 (pg. 
49
-
57
)
16
Faustino
 
N.A.
Cooper
 
T.A.
 
Pre-mRNA splicing and human disease
Genes Dev.
2003
, vol. 
17
 (pg. 
419
-
437
)
17
Stoilov
 
P.
Meshorer
 
E.
Gencheva
 
M.
Glick
 
D.
Soreq
 
H.
Stamm
 
S.
 
Defects in pre-mRNA processing as causes of and predisposition to diseases
DNA Cell Biol.
2002
, vol. 
21
 (pg. 
803
-
818
)
18
Venables
 
J.P.
 
Unbalanced alternative splicing and its significance in cancer
BioEssays
2006
, vol. 
28
 (pg. 
378
-
386
)
19
Hagiwara
 
M.
 
Alternative splicing: a new drug target of the post-genome era
Biochim. Biophys. Acta
2005
, vol. 
1754
 (pg. 
324
-
331
)
20
Bracco
 
L.
Kearsey
 
J.
 
The relevance of alternative RNA splicing to pharmacogenomics
Trends Biotechnol.
2003
, vol. 
21
 (pg. 
346
-
353
)
21
Hernandez
 
F.
Perez
 
M.
Lucas
 
J.J.
Mata
 
A.M.
Bhat
 
R.
Avila
 
J.
 
Glycogen synthase kinase-3 plays a crucial role in tau exon 10 splicing and intranuclear distribution of SC35: implications for Alzheimer's disease
J. Biol. Chem.
2004
, vol. 
279
 (pg. 
3801
-
3806
)
22
Brichta
 
L.
Hofmann
 
Y.
Hahnen
 
E.
Siebzehnrubl
 
F.A.
Raschke
 
H.
Blumcke
 
I.
Eyupoglu
 
I.Y.
Wirth
 
B.
 
Valproic acid increases the SMN2 protein level: a well-known drug as a potential therapy for spinal muscular atrophy
Hum. Mol. Genet.
2003
, vol. 
12
 (pg. 
2481
-
2489
)
23
Aartsma-Rus
 
A.
van Ommen
 
G.J.
 
Antisense-mediated exon skipping: a versatile tool with therapeutic and research applications
RNA
2007
, vol. 
13
 (pg. 
1609
-
1624
)
24
Eckstein
 
F.
 
The versatility of oligonucleotides as potential therapeutics
Expert Opin. Biol. Ther.
2007
, vol. 
7
 (pg. 
1021
-
1034
)
25
Wirth
 
B.
Brichta
 
L.
Hahnen
 
E.
 
Spinal muscular atrophy: from gene to therapy
Semin. Pediatr. Neurol.
2006
, vol. 
13
 (pg. 
121
-
131
)
26
Chang
 
J.G.
Hsieh-Li
 
H.M.
Jong
 
Y.J.
Wang
 
N.M.
Tsai
 
C.H.
Li
 
H.
 
Treatment of spinal muscular atrophy by sodium butyrate
Proc. Natl. Acad. Sci. U.S.A.
2001
, vol. 
98
 (pg. 
9808
-
9813
)
27
Rossi
 
F.
Labourier
 
E.
Forne
 
T.
Divita
 
G.
Derancourt
 
J.
Riou
 
J.F.
Antione
 
E.
Cathela
 
G.
Brunel
 
C.
Tazi
 
J.
 
Specific phosphorylation of SR proteins by mammalian DNA topoisomerase I
Nature
1996
, vol. 
381
 (pg. 
80
-
82
)
28
Tazi
 
J.
Rossi
 
F.
Labourier
 
E.
Gallouzi
 
I.
Brunel
 
C.
Antoine
 
E.
 
DNA topoisomerase I: customs officer at the border between DNA and RNA worlds?
J. Mol. Med.
1997
, vol. 
75
 (pg. 
786
-
800
)
29
Muraki
 
M.
Ohkawara
 
B.
Hosoya
 
T.
Onogi
 
H.
Koizumi
 
J.
Koizumi
 
T.
Sumi
 
K.
Yomoda
 
J.I.
Murray
 
M.V.
Kimura
 
H.
, et al 
Manipulation of alternative splicing by a newly developed inhibitor of Clks
J. Biol. Chem.
2004
, vol. 
279
 (pg. 
24246
-
24254
)
30
Fukuhara
 
T.
Hosoya
 
T.
Shimizu
 
S.
Sumi
 
K.
Oshiro
 
T.
Yoshinaka
 
Y.
Suzuki
 
M.
Yamamoto
 
N.
Herzenberg
 
L.A.
Hagiwara
 
M.
 
Utilization of host SR protein kinases and RNA-splicing machinery during viral replication
Proc. Natl. Acad. Sci. U.S.A.
2006
, vol. 
103
 (pg. 
11329
-
11333
)
31
Gasparini
 
L.
Terni
 
B.
Spillantini
 
M.G.
 
Frontotemporal dementia with tau pathology
Neurodegener. Dis.
2007
, vol. 
4
 (pg. 
236
-
253
)
32
Novoyatleva
 
T.
Heinrich
 
B.
Tang
 
Y.
Benderska
 
N.
Butchbach
 
M.E.
Lorson
 
C.L.
Lorson
 
M.A.
Ben-Dov
 
C.
Fehlbaum
 
P.
Bracco
 
L.
, et al 
Protein phosphatase 1 binds to the RNA recognition motif of several splicing factors and regulates alternative pre-mRNA processing
Hum. Mol. Genet.
2008
, vol. 
17
 (pg. 
52
-
70
)
33
Chalfant
 
C.E.
Rathman
 
K.
Pinkerman
 
R.L.
Wood
 
R.E.
Obeid
 
L.M.
Ogretmen
 
B.
Hannun
 
Y.A.
 
De novo ceramide regulates the alternative splicing of caspase 9 and Bcl-x in A549 lung adenocarcinoma cells: dependence on protein phosphatase-1
J. Biol. Chem.
2002
, vol. 
277
 (pg. 
12587
-
12595
)
34
Angelozzi
 
C.
Borgo
 
F.
Tiziano
 
F.D.
Martella
 
A.
Neri
 
G.
Brahe
 
C.
 
Salbutamol increases SMN mRNA and protein levels in spinal muscular atrophy cells
J. Med. Genet.
2007
, vol. 
45
 (pg. 
29
-
31
)
35
Lunn
 
M.R.
Root
 
D.E.
Martino
 
A.M.
Flaherty
 
S.P.
Kelley
 
B.P.
Coovert
 
D.D.
Burghes
 
A.H.
Man
 
N.T.
Morris
 
G.E.
Zhou
 
J.
, et al 
Indoprofen upregulates the survival motor neuron protein through a cyclooxygenase-independent mechanism
Chem. Biol.
2004
, vol. 
11
 (pg. 
1489
-
1493
)
36
Auboeuf
 
D.
Honig
 
A.
Berget
 
S.M.
O'Malley
 
B.W.
 
Coordinate regulation of transcription and splicing by steroid receptor coregulators
Science
2002
, vol. 
298
 (pg. 
416
-
419
)
37
Dowhan
 
D.H.
Hong
 
E.P.
Auboeuf
 
D.
Dennis
 
A.P.
Wilson
 
M.M.
Berget
 
S.M.
O'Malley
 
B.W.
 
Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERα and CAPERβ
Mol. Cell
2005
, vol. 
17
 (pg. 
429
-
439
)
38
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 SR protein splicing factors
Proc. Natl. Acad. Sci. U.S.A.
2005
, vol. 
102
 (pg. 
8764
-
8769
)
39
Bakkour
 
N.
Lin
 
Y.L.
Maire
 
S.
Ayadi
 
L.
Mahuteau-Betzer
 
F.
Nguyen
 
C.H.
Mettling
 
C.
Portales
 
P.
Grierson
 
D.
Chabot
 
B.
, et al 
Small-molecule inhibition of HIV pre-mRNA splicing as a novel antiretroviral therapy to overcome drug resistance
PLoS Pathog.
2007
, vol. 
3
 (pg. 
1530
-
1539
)
40
Xie
 
J.
Black
 
D.L.
 
A CaMK IV responsive RNA element mediates depolarization-induced alternative splicing of ion channels
Nature
2001
, vol. 
410
 (pg. 
936
-
939
)
41
Andreassi
 
C.
Angelozzi
 
C.
Tiziano
 
F.D.
Vitali
 
T.
De Vincenzi
 
E.
Boninsegna
 
A.
Villanova
 
M.
Bertini
 
E.
Pini
 
A.
Neri
 
G.
Brahe
 
C.
 
Phenylbutyrate increases SMN expression in vitro: relevance for treatment of spinal muscle atrophy
Eur. J. Hum. Genet.
2004
, vol. 
12
 (pg. 
59
-
65
)
42
Riessland
 
M.
Brichta
 
L.
Hahnen
 
E.
Wirth
 
B.
 
The benzamide M344, a novel histone deacetylase inhibitor, significantly increases SM2 RNA/protein levels in spinal muscular atrophy cells
Hum. Genet.
2006
, vol. 
120
 (pg. 
101
-
110
)
43
Hahnen
 
E.
Eyupoglu
 
I.Y.
Brichta
 
L.
Haastert
 
K.
Trankle
 
C.
Siebzehnrubl
 
F.A.
Riessland
 
M.
Holker
 
I.
Claus
 
P.
Romstock
 
J.
, et al 
In vitro and ex vivo evaluation of second-generation histone deacetylase inhibitors for the treatment of spinal muscular atrophy
J. Neurochem.
2006
, vol. 
98
 (pg. 
193
-
202
)
44
Andreassi
 
C.
Jarecki
 
J.
Zhou
 
J.
Coovert
 
D.D.
Monani
 
U.R.
Chen
 
X.
Witney
 
M.
Pollok
 
B.
Zhang
 
M.
Androphy
 
E.
Burghes
 
A.H.
 
Aclarubicin treatment restores SMN levels to cells derived from type I spinal muscular atrophy patients
Hum. Mol. Genet.
2001
, vol. 
10
 (pg. 
2841
-
2849
)
45
Solier
 
S.
Lansiaux
 
A.
Logette
 
E.
Wu
 
J.
Soret
 
J.
Tazi
 
J.
Bailly
 
C.
Desoche
 
L.
Solary
 
E.
Corcos
 
L.
 
Topoisomerase I and II inhibitors control caspase-2 pre-messenger RNA splicing in human cells
Mol. Cancer Res.
2004
, vol. 
2
 (pg. 
53
-
61
)
46
Pilch
 
B.
Allemand
 
E.
Facompre
 
M.
Bailly
 
C.
Riou
 
J.F.
Soret
 
J.
Tazi
 
J.
 
Specific inhibition of serine- and arginine-rich splicing factors phosphorylation, spliceosome assembly, and splicing by the antitumor drug NB-506
Cancer Res.
2001
, vol. 
61
 (pg. 
6876
-
6884
)
47
Ting
 
C.Y.
Hsu
 
C.T.
Hsu
 
H.T.
Su
 
J.S.
Chen
 
T.Y.
Tarn
 
W.Y.
Kuo
 
Y.H.
Whang-Peng
 
J.
Liu
 
L.F.
Hwang
 
J.
 
Isodiospyrin as a novel human DNA topoisomerase I inhibitor
Biochem. Pharmacol.
2003
, vol. 
66
 (pg. 
1981
-
1991
)
48
Bhat
 
R.
Xue
 
Y.
Berg
 
S.
Hellberg
 
S.
Ormo
 
M.
Nilsson
 
Y.
Radesater
 
A.C.
Jerning
 
E.
Markgren
 
P.O.
Borgegard
 
T.
, et al 
Structural insights and biological effects of glycogen synthase kinase 3-specific inhibitor AR-A014418
J. Biol. Chem.
2003
, vol. 
278
 (pg. 
45937
-
45945
)
49
Zhang
 
M.L.
Lorson
 
C.L.
Androphy
 
E.J.
Zhou
 
J.
 
An in vivo reporter system for measuring increased inclusion of exon 7 in SMN2 mRNA: potential therapy of SMA
Gene. Ther.
2001
, vol. 
8
 (pg. 
1532
-
1538
)
50
Kosaki
 
A.
Webster
 
N.J.
 
Effect of dexamethasone on the alternative splicing of the insulin receptor mRNA and insulin action in HepG2 hepatoma cells
J. Biol. Chem.
1993
, vol. 
268
 (pg. 
21990
-
21996
)
51
Lai
 
G.J.
McCobb
 
D.P.
 
Opposing actions of adrenal androgens and glucocorticoids on alternative splicing of Slo potassium channels in bovine chromaffin cells
Proc. Natl. Acad. Sci. U.S.A.
2002
, vol. 
99
 (pg. 
7722
-
7727
)
52
Yuo
 
C.Y.
Lin
 
H.H.
Chang
 
Y.S.
Yang
 
W.K.
Chang
 
J.G.
 
5-(N-ethyl-N-isopropyl)-amiloride enhances SMN2 exon 7 inclusion and protein expression in spinal muscular atrophy cells
Ann. Neurol.
2008
, vol. 
63
 (pg. 
26
-
34
)
53
Sgambato
 
V.
Minassian
 
R.
Nairn
 
A.C.
Hyman
 
S.E.
 
Regulation of ania-6 splice variants by distinct signaling pathways in striatal neurons
J. Neurochem.
2003
, vol. 
86
 (pg. 
153
-
164
)
54
Meshul
 
C.K.
Bunker
 
G.L.
Mason
 
J.N.
Allen
 
C.
Janowsky
 
A.
 
Effects of subchronic clozapine and haloperidol on striatal glutamatergic synapses
J. Neurochem.
1996
, vol. 
67
 (pg. 
1965
-
1973
)
55
Grzeschik
 
S.M.
Ganta
 
M.
Prior
 
T.W.
Heavlin
 
W.D.
Wang
 
C.H.
 
Hydroxyurea enhances SMN2 gene expression in spinal muscular atrophy cells
Ann. Neurol.
2005
, vol. 
58
 (pg. 
194
-
202
)
56
Walter
 
H.J.
McMahon
 
T.
Dadgar
 
J.
Wang
 
D.
Messing
 
R.O.
 
Ethanol regulates calcium channel subunits by protein kinase Cδ-dependent and -independent mechanisms
J. Biol. Chem.
2000
, vol. 
275
 (pg. 
25717
-
25722
)
57
Bolduc
 
L.
Labrecque
 
B.
Cordeau
 
M.
Blanchette
 
M.
Chabot
 
B.
 
Dimethyl sulfoxide affects the selection of splice sites
J. Biol. Chem.
2001
, vol. 
276
 (pg. 
17597
-
17602
)
58
Slaugenhaupt
 
S.A.
Mull
 
J.
Leyne
 
M.
Cuajungco
 
M.P.
Gill
 
S.P.
Hims
 
M.M.
Quintero
 
F.
Axelrod
 
F.B.
Gusella
 
J.F.
 
Rescue of a human mRNA splicing defect by the plant cytokinin kinetin
Hum. Mol. Genet.
2004
, vol. 
13
 (pg. 
429
-
436
)
59
Montecucco
 
A.
Biamonti
 
G.
 
Cellular response to etoposide treatment
Cancer Lett.
2007
, vol. 
252
 (pg. 
9
-
18
)
60
Sakla
 
M.S.
Lorson
 
C.L.
 
Induction of full-length survival motor neuron by polyphenol botanical compounds
Hum. Genet.
2008
, vol. 
122
 (pg. 
635
-
643
)
61
Anderson
 
S.L.
Qiu
 
J.
Rubin
 
B.Y.
 
EGCG corrects aberrant splicing of IKAP mRNA in cells from patients with familial dysautonomia
Biochem. Biophys. Res. Commun.
2003
, vol. 
310
 (pg. 
627
-
633
)