Splicing of the c-src N1 exon in neuronal cells depends in part on an intronic cluster of RNA regulatory elements called the downstream control sequence (DCS). Using site-specific cross-linking, RNA gel shift, and DCS RNA affinity chromatography assays, we characterized the binding of several proteins to specific sites along the DCS RNA. Heterogeneous nuclear ribonucleoprotein (hnRNP) H, polypyrimidine tract binding protein (PTB), and KH-type splicing-regulatory protein (KSRP) each bind to distinct elements within this sequence. We also identified a new 60-kDa tissue-specific protein that binds to the CUCUCU splicing repressor element of the DCS RNA. This protein was purified, partially sequenced, and cloned. The new protein (neurally enriched homolog of PTB [nPTB]) is highly homologous to PTB. Unlike PTB, nPTB is enriched in the brain and in some neural cell lines. Although similar in sequence, nPTB and PTB show significant differences in their properties. nPTB binds more stably to the DCS RNA than PTB does but is a weaker repressor of splicing in vitro. nPTB also greatly enhances the binding of two other proteins, hnRNP H and KSRP, to the DCS RNA. These experiments identify specific cooperative interactions between the proteins that assemble onto an intricate splicing-regulatory sequence and show how this hnRNP assembly is altered in different cell types by incorporating different but highly related proteins.Alternative splicing is a common mechanism for regulating gene expression in eukaryotes, allowing the generation of diverse proteins from the same primary RNA transcript (46,77,78). The alteration of splice site choice is thought to be determined by regulatory proteins that bind to the pre-mRNA transcript and affect spliceosome assembly on particular exons or splice sites. The best characterized of these splicing-regulatory proteins are a set of polypeptides called SR proteins that, among many other properties, bind to exonic splicing enhancer sequences (7,10,35,47,75). The SR proteins bound to an exonic enhancer are thought to stimulate spliceosome assembly at the adjacent splice sites. Another group of pre-mRNA binding proteins are the heterogeneous nuclear ribonucleoproteins (hnRNPs) (19,66). These are a diverse group of molecules that coat nascent pre-mRNAs, forming complex but little understood hnRNP structures (42, 52). The assembly of the spliceosome occurs after formation of these hnRNP complexes, and some hnRNPs have been implicated in splicing regulation. For example, hnRNP A1 is able to counteract the effect of SR proteins in some assays and can also apparently repress splicing through splicing silencer sequences (3,7,8,11,31). However, the assembly of a pre-mRNP complex is poorly understood. It is apparently highly cooperative, but the interactions between the different hnRNPs in these complexes are mostly unknown.Although widely expressed, the SR proteins and hnRNPs do vary in concentration between different tissues (31, 39). Changes in splicing patterns are thought to be determined, in part, ...

We have purified and cloned a new splicing factor, KSRP. KSRP is a component of a multiprotein complex that binds specifically to an intronic splicing enhancer element downstream of the neuron-specific c-src N1 exon. This 75-kD protein induces the assembly of five other proteins, including the heterogeneous nuclear ribonucleoprotein F, onto the splicing enhancer. The sequence of the KSRP cDNA indicates that the protein contains four K homology RNA-binding domains and an unusual carboxy-terminal domain. KSRP is similar to two proteins, FUSE-binding protein and P-element somatic inhibitor. KSRP is expressed in both neural and non-neural cell lines, although it is present at higher levels in neural cells. Antibodies specific for KSRP inhibit the splicing of the N1 exon in vitro. Moreover, this inhibition of N1 splicing can be rescued by the addition of purified KSRP. KSRP is likely to regulate splicing from a number of intronic splicing enhancer sequences.[Key Words: Alternative splicing; regulatory protein; KSRP; intronic splicing enhancer; RNA-binding protein]

We studied the role of polypyrimidine tract binding protein in repressing splicing of the c-src neuron-specific N1 exon. Immunodepletion/add-back experiments demonstrate that PTB is essential for splicing repression in HeLa extract. When splicing is repressed, PTB cross-links to intronic CUCUCU elements flanking the N1 exon. Mutation of the downstream CU elements causes dissociation of PTB from the intact upstream CU elements and allows splicing. Thus, PTB molecules bound to multiple elements cooperate to repress splicing. Interestingly, in neuronal WERI-1 cell extract where N1 is spliced, PTB also binds to the upstream CU elements but is dissociated in the presence of ATP. We conclude that splicing repression by PTB is modulated in different cells by a combination of cooperative binding and ATP-dependent dissociation.

Alternative splicing has emerged as a promising therapeutic target in a number of human disorders. However, the discovery of compounds that target the splicing reaction has been hindered by the lack of suitable high-throughput screening assays. Conversely, the effects of known drugs on the splicing reaction are mostly unclear and not routinely assessed. We have developed a twocolor fluorescent reporter for cellular assays of exon inclusion that can accommodate nearly any cassette exon and minimizes interfering effects from changes in transcription and translation. We used microtubule-associated protein tau (MAPT) exon 10, whose missplicing causes frontotemporal dementia, to test the reporter in screening libraries of known bioactive compounds. These screens yielded several compounds that alter the splicing of the exon, both in the reporter and in the endogenous MAPT mRNA. One compound, digoxin, has long been used in the treatment of heart failure, but was not known to modulate splicing. The positive compounds target different signal transduction pathways, and microarray analysis shows that each compound affects the splicing of a different set of exons in addition to MAPT exon 10. Our results identify currently prescribed cardiotonic steroids as modulators of alternative splicing and demonstrate the feasibility of screening for drugs that alter exon inclusion.digoxin ͉ fluorescent reporter ͉ plant steroids ͉ MAPT ͉ FTDP-17 D isruption of exon recognition and misregulation of alternative splicing are a common cause of human disease. Conditions linked to errors in pre-mRNA splicing include autoimmune disorders, neurodegenerative diseases, cystic fibrosis, growth hormone deficiency, muscular dystrophy, and cancer progression (1-3). Thus, the RNA splicing machinery is an important potential target for drug development. However, few drugs have been identified that specifically target the splicing reaction, and the impact of existing drugs on splicing regulation is not routinely examined.One disease stemming from misregulation of alternative splicing is frontotemporal dementia with parkinsonism on chromosome 17 (FTDP-17) (4). FTDP-17 is caused by mutations affecting exon 10 of the microtubule-associated protein tau (MAPT) gene that increase inclusion of exon 10 in the mRNA. Exon 10 encodes the fourth microtubule-binding domain of the protein, and elevated levels of the four-domain form of tau evidently lead to neurofibrillary tangles and subsequent neurodegeneration. Thus, there is significant therapeutic interest in modulating the splicing of this exon. Multiple factors are known to affect MAPT exon 10 splicing (4-9). This combinatorial control is typical of alternative splicing patterns and points to the difficulties in developing splicingtargeted therapeutics. Interfering with individual factors often only partially affects a given splicing pattern, and each factor can affect many unrelated exons in addition to the therapeutic target.Finding compounds that modulate alternative splicing requires effective high-throug...

CaV1.2 voltage-gated calcium channels play critical roles in the control of membrane excitability, gene expression, and muscle contraction. These channels show diverse functional properties generated by alternative splicing at multiple sites within the CaV1.2 pre-mRNA. The molecular mechanisms controlling this splicing are not understood. We find that two exons in the CaV1.2 channel are controlled in part by members of the Fox family of splicing regulators. Exons 9* and 33 confer distinct electrophysiological properties on the channel and show opposite patterns of regulation during cortical development, with exon 9* progressively decreasing its inclusion in the CaV1. CaV1.2 L-type voltage-gated calcium channels are widely distributed in brain, heart, smooth muscle, and endocrine cells and play essential roles in gene expression, muscle contraction, and hormone release (6,13,16,39,47). These channels are composed of three subunits, with the ␣ 1 subunit being the largest and incorporating the conduction pore, the voltage sensor and gating apparatus, as well as sites for channel regulation by second messengers, drugs, and toxins (Fig. 1A) (9,14,17). This CaV1.2 subunit is subject to extensive alternative splicing that generates multiple functionally distinct isoforms (1,29,33,49,62). At least twenty of the 56 exons in the human CaV1.2 transcript are alternatively spliced (29,50,51,55). In particular, alternative exon 9* within the cytoplasmic I-II loop and exon 33 within the IVS3-IVS4 transmembrane segments confer different electrophysiological and pharmacological properties on the channel and exhibit tissue-specific differences in inclusion (30,31,54,55). Changes in exon 9* (also named exon 9A) splicing are seen in human arterial smooth muscle cells that have developed atherosclerosis (57) and in hypertrophied cardiomyocytes of spontaneously hypertensive rats (56). Alternative exons 9* and 33 are conserved across vertebrate species demonstrating their functional importance to the CaV1.2 channel. However, the molecular mechanisms controlling their splicing have not been studied.Members of the Fox protein family, homologs of the Feminizing on the X gene product from Caenorhabditis elegans (21,41,48), regulate the splicing of many neuron-and musclespecific splicing events (22,40,59,(63)(64)(65)(66). There are three mammalian family members, Fox1 (A2BP1), Fox2 (RBM9), and Fox3 (hnrbp3), each containing a nearly identical RNAbinding domain that recognizes the hexanucleotide element UGCAUG (2). These proteins bind the introns adjacent to their target exons where they generally repress splicing when bound upstream of the exon but enhance splicing from a downstream binding site (22,40,59,63,64,66). In addition to the RNA-binding domain, all three proteins have similar N and C-terminal domains that are extensively modified by alternative promoter use and alternative splicing to produce a large family of related proteins. Fox1 is expressed in neurons and muscle, and Fox3 is expressed only in neurons (22,23,36,59). Fox2 show...

CaV1.2 calcium channels play roles in diverse cellular processes such as gene regulation, muscle contraction, and membrane excitation and are diversified in their activity through extensive alternative splicing of the CaV1.2 mRNA. The mutually exclusive exons 8a and 8 encode alternate forms of transmembrane segment 6 (IS6) in channel domain 1. The human genetic disorder Timothy syndrome is caused by mutations in either of these two CaV1.2 exons, resulting in disrupted Ca2+ homeostasis and severe pleiotropic disease phenotypes. The tissue-specific pattern of exon 8/8a splicing leads to differences in symptoms between patients with exon 8 or 8a mutations. Elucidating the mechanisms controlling the exon 8/8a splicing choice will be important in understanding the spectrum of defects associated with the disease. We found that the polypyrimidine tract-binding protein (PTB) mediates a switch from exon 8 to 8a splicing. PTB and its neuronal homolog, nPTB, are widely studied splicing regulators controlling large sets of alternative exons. During neuronal development, PTB expression is down-regulated with a concurrent increase in nPTB expression. Exon 8a is largely repressed in embryonic mouse brain but is progressively induced during neuronal differentiation as PTB is depleted. This splicing repression is mediated by the direct binding of PTB to sequence elements upstream of exon 8a. The nPTB protein is a weaker repressor of exon 8a, resulting in a shift in exon choice when nPTB replaces PTB in cells. These results provide mechanistic understanding of how these two exons, important for human disease, are controlled.

We have developed a simple two-dimensional YAC pooling strategy to facilitate YAC library screening via STS and Alu-PCR approaches. The method has been implemented using the human total genomic YAC library of Olson and coworkers, and its validity tested by isolation of many chromosomes 19- and 21-specific YACs. The Alu-PCR approach is notable in that it is hybridization-based, such that PCR primer pairs do not need to be repeatedly synthesized and tested for each screening step.

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