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Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

This article has been updated

Key Points

  • Alternative splicing is a crucial mechanism for gene regulation and for generating proteomic diversity, which allows individual genes to generate multiple mature mRNA isoforms that can be translated into functionally different proteins. Alternative splicing can be regulated at different stages of spliceosome assembly and by different mechanisms.

  • Splice site recognition of alternative exons is frequently regulated by cooperative interactions between factors such as SR (Ser–Arg) proteins and heterogeneous nuclear ribonucleoprotein particles (hnRNPs), which have lower affinities and sequence specificities. Splice site selection is also influenced by the secondary structure of mRNAs.

  • Two models have been proposed to explain the role of RNA polymerase II in alternative splicing regulation: a recruitment model and a kinetic model, and the two models are not mutually exclusive.

  • Alternative splicing, including tissue-specific alternative splicing, is an extremely common regulatory mechanism. However, the number of known sequence-specific alternative splicing factors (<50) is much smaller than that of sequence-specific transcription factors (2,500). Although more specific splicing factors will undoubtedly be discovered, this disparity suggests important differences in the pathways regulating transcription and splicing.

  • Core spliceosomal proteins can also regulate tissue-specific alternative splicing. This may reflect differential sensitivity of alternative exons to these factors and/or differential accumulation of the factors in different tissues.

  • Post-translational modifications of splicing factors enable cells to switch between alternative splicing isoforms rapidly after environmental stimuli. Phosphorylation can change the intracellular localization of splicing factor, protein–protein and protein–RNA interactions and even intrinsic splicing factor activity.

Abstract

Alternative splicing of mRNA precursors provides an important means of genetic control and is a crucial step in the expression of most genes. Alternative splicing markedly affects human development, and its misregulation underlies many human diseases. Although the mechanisms of alternative splicing have been studied extensively, until the past few years we had not begun to realize fully the diversity and complexity of alternative splicing regulation by an intricate protein–RNA network. Great progress has been made by studying individual transcripts and through genome-wide approaches, which together provide a better picture of the mechanistic regulation of alternative pre-mRNA splicing.

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Figure 1: Mechanisms of alternative splicing by splice site selection.
Figure 2: Phosphorylation switches the general splicing repressor SRp38 into a sequence-specific activator.
Figure 3: Mechanisms of alternative splicing regulation at the transition from exon definition to intron definition.

Change history

  • 12 October 2009

    In the version of this article initially published online the binding sequences for hnRNP G and hnRNP Q in Table 1 were incorrect. This error has been corrected for the print, HTML and PDF versions of the article.

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Acknowledgements

Work from the authors' laboratory was supported in part by grants from the National Institutes of Health. We thank C. David for comments on the manuscript.

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Glossary

Small nuclear ribonucleoprotein particle

(snRNP). A protein, including U1, U2, U4, U5 and U6, which contains U-rich small nuclear RNAs (snRNAs) and both small nuclear ribonucleoprotein (snRNP)-specific and common proteins, and is a core component of the spliceosome.

Branch point

A nucleotide, usually an adenosine, within a variably conserved branch point sequence upstream of the 3′ splice site, the 2′ hydroxyl group of which attacks the 5′ splice site in the first step of splicing.

SR (Ser–Arg) protein family

A family of nuclear factors that have many important roles in splicing mRNA precursors in metazoan organisms, functioning in both constitutive and alternative splicing.

Heterologous nuclear RNP

(hnRNP). A pre-mRNA- or mRNA-binding protein that associates with transcripts during or after transcription and influences their function and fate. Some hnRNPs shuttle in and out of nuclei, whereas others are constitutively nuclear.

Alternative exon

An exon that is included in mature mRNA in certain cellular contexts but excluded in others.

RS (Arg–Ser repeat-containing) domain

A protein domain that is variable in length and enriched in Arg–Ser dipeptides and seems to be involved in protein–protein and protein–RNA interactions.

Hu/ELAV family protein

A protein belonging to a family of nervous system-specific RNA-binding proteins that specifically bind to AU-rich sequences.

CLIP

A method that combines cross-linking and immunoprecipitation to identify in vivo targets of RNA-binding proteins.

RRM domain

(RNA recognition motif domain). A protein domain that is frequently involved in sequence-specific single-stranded RNA binding. Also known as an RNP-type RNA-binding domain.

14-3-3 protein

A protein belonging to a family of conserved proteins that bind to phosphorylated serine and threonine residues and that are encoded by seven genes in most mammals. They bind diverse regulatory proteins, including kinases, phosphatases and transmembrane receptors.

SELEX

A technique to determine the DNA or RNA sequence that is specifically recognized by a protein. The method involves multiple rounds of binding to an initially random sequence until a high-affinity consensus sequence emerges.

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Chen, M., Manley, J. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 10, 741–754 (2009). https://doi.org/10.1038/nrm2777

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