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Functional consequences of developmentally regulated alternative splicing

Key Points

  • A large fraction of genes in worms, flies and vertebrates express multiple mRNAs by alternative splicing. This produces extensive mRNA structural diversity that ultimately affects protein coding potential as well as mRNA cis-acting elements that are determinative for translation, mRNA stability and mRNA intracellular localization.

  • Global analyses of alternative splicing regulation during periods of biological transition, such as during development, have revealed coordinated and conserved networks of alternative splicing.

  • Several splicing regulatory networks controlled by individual RNA-binding proteins have been identified by combining recent advances in genome-wide analyses of alternative splicing with the identification of RNA binding sites in vivo.

  • A high proportion of RNA-binding proteins that regulate alternative splicing are themselves regulated by alternative splicing and are subject to auto- and crossregulatory feedback. This type of regulation includes alternative splicing linked with nonsense-mediated decay (AS–NMD), which results in mRNA downregulation.

  • Diverse physiological processes are regulated in a determinative fashion by alternative splicing patterns, including meiosis in budding yeast, neuronal arborization in the Drosophila melanogaster brain, and stem cell determination in vertebrates.

  • The regulation of gene expression by alternative splicing is intricately linked with transcription, the epigenetic state of chromatin, and subsequent RNA processing events, such as 3′ end formation, mRNA export and mRNA translation efficiency.

Abstract

Genome-wide analyses of metazoan transcriptomes have revealed an unexpected level of mRNA diversity that is generated by alternative splicing. Recently, regulatory networks have been identified through which splicing promotes dynamic remodelling of the transcriptome to promote physiological changes, which involve robust and coordinated alternative splicing transitions. The regulation of splicing in yeast, worms, flies and vertebrates affects a variety of biological processes. The functional classes of genes that are regulated by alternative splicing include both those with widespread homeostatic activities and those with cell-type-specific functions. Alternative splicing can drive determinative physiological change or can have a permissive role by providing mRNA variability that is used by other regulatory mechanisms.

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Figure 1: Role of splicing regulation during early meiosis in Saccharomyces cerevisiae.
Figure 2: Integration of alternative splicing with epithelial-to-mesenchymal transitions.
Figure 3: Coordinated alternative splicing changes drive fetal-to-adult transitions during postnatal heart development.

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Acknowledgements

T.A.C. is supported by the US National Institutes of Health (AR045653, AR060733, HL045565) and the Muscular Dystrophy Association (156780). A.K. is supported by a Scientist Development Grant from the American Heart Association (11SDG4980011).

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Glossary

Transcriptomes

The transcriptome technically refers to all of the RNA in a cell; however, the term is often used to describe the polyadenylated RNAs transcribed by RNA polymerase II, which are selected for analysis by oligo(dT).

RNA sequencing

(RNA-seq). High-throughput shotgun sequencing of cDNA to obtain the sequence of the transcriptome.

mRNA structural complexity

The number and ratio of different transcripts produced from each gene. It is one component of mRNA complexity, along with the number of genes that produce transcripts and the abundance of the transcripts from each gene.

Nonsense-mediated decay

(NMD). An mRNA surveillance mechanism that degrades mRNAs containing nonsense mutations to prevent the expression of truncated or erroneous proteins.

Spliceosome

The complex and conserved nuclear machinery that removes introns. The spliceosome contains five small uridylate-rich small nuclear RNAs (UsnRNAs) and ~150 proteins.

SR proteins

A highly conserved family of RNA-binding proteins that contain arginine/serine-rich domains. They function in constitutive as well as alternative splicing and are primarily splicing activators.

CLIP

A biochemical technique that uses ultraviolet crosslinking of protein and RNA in vivo followed by immunoprecipitation to identify direct protein–RNA interaction sites in living cells.

Core pluripotency factors

A set of transcription factors (including OCT4, NANOG, SOX2 and TCF3) that form a core transcriptional circuit to maintain the pluripotent state of embryonic stem cells.

MicroRNA

(miRNA). An evolutionarily conserved small non-coding RNA (~22 nucleotides long) that silences gene expression by degrading or inhibiting translation of mRNA transcripts in a sequence-specific manner.

Epithelial-to-mesenchymal transitions

(EMTs). Phenotypic conversions that disrupt the polarity of epithelial cells to establish invasive mesenchymal features through alterations in cytoskeletal organization, cell adhesion and the extracellular matrix.

Histone code

Post-translational modifications of histone proteins that regulate the accessibility of chromatin-bound DNA to the general transcription machinery to provide an instructive code for cell- and tissue-specific gene expression.

Dicer1

A gene encoding the endoribonuclease Dicer that cleaves double-stranded RNAs to produce small interfering RNAs and microRNAs with a two-nucleotide overhang at the 3′ end.

Arborization

A tree-like branching process through which a neuron expands its dendritic coverage in three-dimensional space to integrate multiple synaptic or sensory inputs.

Commissural neurons

Neurons that cross the midline of the brain to connect the right and left brain hemispheres.

Heterogeneous nuclear ribonucleoprotein

A conserved family of RNA-binding proteins, many of which are highly abundant, that tend to repress splicing.

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Kalsotra, A., Cooper, T. Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet 12, 715–729 (2011). https://doi.org/10.1038/nrg3052

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