Trends in Genetics
ReviewAlternative splicing: multiple control mechanisms and involvement in human disease
Section snippets
The SR family of proteins
The SR proteins, a group of highly conserved proteins in metazoans, are required for constitutive splicing and also influence alternative splicing regulation 8., 9.. They have a modular structure consisting of one or two copies of an RNA-recognition motif (RRM) and a C-terminal domain rich in alternating serine and arginine residues (the RS domain). The RRMs determine RNA-binding specificity, whereas the RS domain mediates protein–protein interactions that are thought to be essential for the
Actions of SR proteins and hnRNP A/B proteins in splice site selection
The first SR proteins to be identified had similar effects on 5′ splice-site selection: increased concentrations of the proteins resulted in the selection of intron-proximal 5′ splice sites in pre-mRNAs that contain two or more alternative 5′ splice sites. Strikingly, an excess of hnRNP A/B proteins had the opposite effect, promoting the selection of intron-distal 5′ splice sites. These effects have been observed with different pre-mRNA substrates both in vitro and in vivo 13., 14., 15..
Polypyrimidine tract binding protein (PTB)
Polypyrimidine tract binding protein (PTB) (also known as hnRNP I) is an RNA binding protein that recognizes polypyrimidine tracts preceding 3′ splice sites and has a role as a negative regulator of splicing. PTB represses several neuron-specific exons in non-neuronal cells, as well as smooth muscle-specific inclusion of alternatively spliced exons in the α-tropomyosin and α-actinin pre-mRNAs. PTB and U2AF competitive binding to the polypyrimidine tract has been proposed as the basis for the
The CELF protein family
The CELF family of proteins (CUG-BP and ETR3-like factors) are involved in cell-specific and developmentally regulated alternative splicing [35]. These RNA-binding proteins contain three RRMs and a divergent linker domain of unknown function. The expression of two CELF proteins, CELF3 and CELF5, is restricted to brain; whereas CUG-BP, ETR-3 and CELF4 are more broadly expressed, although their expression is developmentally regulated in striated muscle and brain. CELF proteins bind to
Tissue-specific factors
The antagonistic effects of general splicing factors, such as SR proteins and hnRNP proteins, can explain a large variety of splicing decisions. However, it is most likely that tissue-specific or developmentally regulated splicing factors have an important role in the regulation of alternative splicing, as is the case in Drosophila. However, progress in the identification of such factors in mammalian systems has been slow.
Alternative splicing is widely used in the nervous system 36., 37..
Role of transcription in alternative splicing
Recent evidence indicates that alternative splicing might be regulated not only by the relative abundance of antagonistic factors, but also by a more complex process involving the transcription machinery. In fact, transcription and pre-mRNA processing are not independent events. On the contrary, there is a high degree of coordination in both time and space because all three processing reactions (capping, splicing and cleavage/polyadenylation) occur in intimate association with the elongating
Molecular models for the coupling between transcription and alternative splicing
A possible mechanism that would fit these results is that the promoter itself is responsible for recruiting splicing factors, such as SR family proteins, to the site of transcription, possibly through transcription factors that bind the promoter or the transcriptional enhancers (Fig. 2a). The finding that p52, a transcriptional coactivator, directly interacts with SF2/ASF stimulating pre-mRNA splicing is consistent with this model [49]. Furthermore, some proteins could have a dual function,
Alternative splicing and disease
Mutations located in noncoding regions, such as those affecting 5′ and 3′ splice sites, branch sites or polyadenylation signals, are frequently the cause of hereditary disease. Approximately 15% of mutations that cause genetic disease affect pre-mRNA splicing [62]. Nonsense mutations that provoke premature termination codons, far from allowing the synthesis of shorter nonfunctional proteins, target the mRNA for degradation nonsense-mediated decay (NMD), which involves an mRNA quality-control
Repeats in cis and in trans
Repetitive di- or trinucleotide sequences are scattered over the human genome. Dinucleotide microsatellites are usually found in intergenic regions and represent length-based polymorphisms with little phenotypic influence. By contrast, trinucleotide repeats, generally intragenic, present dynamic expansions that are the cause of many hereditary diseases such as Huntington's disease and myotonic dystrophy. We will discuss two examples that illustrate how repeats can provoke disease-associated
Conclusions
Complexity, plasticity and functional specialization are distinctive features of multicellular eukaryotic organisms. Until recently it was assumed that these features were mainly achieved through the differential turning on and off of a large number of genes. The realization that the human genome contains a smaller number of genes than expected, and the finding of multiple mechanisms that control the amount and quality of the encoded mRNAs enhance the contribution of pre-mRNA processing, and in
Acknowledgements
We thank Ian Eperon, Nick Hastie and Juan Valcárcel for comments on the manuscript. We acknowledge support from the Medical Research Council (J.F.C.), the Fundación Antorchas, ICGEB, ANPCYT and CONICET (A.R.K.). A.R.K. is an International Research Scholar of the Howard Hughes Medical Institute. We apologize to colleagues whose work was not cited directly owing to space limitations.
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