The search for alternative splicing regulators: new approaches offer a path to a splicing code

David, Charles J.; Manley, James L.

doi:10.1101/gad.1643108

Cited by 49 publications

(38 citation statements)

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“…Tissue-specific alternative splicing events can be explained in part by tissue-specific expression of splicing factors, and the corresponding regulation of their target mRNA transcripts31,119,120. In keeping with this, numerous tissue-specific alternative splicing regulators have now been identified (TABLE 2).…”

Section: Alternative Splicing and Tissue Specificitymentioning

confidence: 86%

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

Chen

Manley

2009

Nat Rev Mol Cell Biol

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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 premRNA splicing.Alternative splicing is a crucial mechanism for gene regulation and for generating proteomic diversity. Recent estimates indicate that the expression of nearly 95% of human multi-exon genes involves alternative splicing 1,2 . In metazoans, alternative splicing plays an important part in generating different protein products that function in diverse cellular processes, including cell growth, differentiation and death.Splicing is carried out by the spliceosome, a massive structure in which five small nuclear ribonucleoprotein particles (snRNPs) and a large number of auxiliary proteins cooperate to accurately recognize the splice sites and catalyse the two steps of the splicing reaction 1,2 (BOX 1). Spliceosome assembly (BOX 1) begins with the recognition of the 5′ splice site by the snRNP U1 and the binding of splicing factor 1 (SF1) to the branch point 3 and of the U2 auxiliary factor (U2AF) heterodimer to the polypyrimidine tract and 3′ terminal AG 4,5 . This assembly is ATP independent and results in the formation of the E complex, which is converted into the ATP-dependent, pre-spliceosomal A complex after the replacement of SF1 by the U2 snRNP at the branch point. Further recruitment of the U4/U6-U5 tri-snRNP complex leads to the formation of the B complex, which is converted into to the catalytically active C complex after extensive conformational changes and remodelling. Splicing and spliceosome assemblyPre-mRNA splicing is a process in which intervening sequences (introns) are removed from an mRNA precursor. Splicing consists of two transesterification steps, each involving a nucleophilic attack on terminal phosphodiester bonds of the intron. In the first step this is carried out by the 2′ hydroxyl of the branch point (usually adenosine) and in the second step by the 3′ hydroxyl of the upstream (5′) exon 1,2 . This process is carried out in the spliceosome, a dynamic molecular machine the assembly of which involves sequential binding and release of small nuclear ribonucleoprotein particles (snRNPs) and numerous protein factors as well as the formation and disruption of RNA-RNA, protein-RNA and protein-protein interactions.The basic mechanics of spliceosome assembly are well known. Briefly, the process begins with the base pairing of U1 snRNA to the 5′ splice site (ss) and the binding of splicing factor 1 (SF1) to the b...

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Section: Alternative Splicing and Tissue Specificitymentioning

confidence: 86%

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

Chen

Manley

2009

Nat Rev Mol Cell Biol

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1,080

802

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“…Several of these regulators have been identified (Wang and Cooper, 2007;David and Manley, 2008), and their role in developmental regulation is perhaps best exemplified by the role of Drosophila Sxl in the sex determination cascade (Penalva and Sanchez, 2003). Given the restricted expression and function of wit, the alternative splicing regulator could also be a ubiquitous one, such as members of the SR proteins and hnRNP families.…”

Section: Bmp Signaling Regulates Mrna Splicing or Stabilitymentioning

confidence: 99%

Identification of downstream targets of the Bone Morphogenetic Protein pathway in the Drosophila nervous system

Kim

Marqués

2010

Developmental Dynamics

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Bone Morphogenetic Protein (BMP) signaling mediated by the receptor Wishful thinking (Wit) is essential for nervous system development in Drosophila. Mutants lacking wit function show defects in neuromuscular junction development and function, specification of neurosecretory phenotypes, and eclosion behavior that result in lethality. The ligand is Glass bottom boat, the Drosophila ortholog of mammalian BMP-7, which acts as a retrograde signal through the Wit receptor. In order to identify transcriptional targets of the BMP pathway in the Drosophila nervous system, we have analyzed the gene expression profile of wit mutant larval central nervous system. Genes differentially expressed identified by microarray analysis have been verified by quantitative PCR and studied by in situ hybridization. Among the genes thus identified, we find solute transporters, neuropeptides, mitochondrial proteins, and novel genes. In addition, several genes are regulated by wit in an isoform-specific manner that suggest regulation of alternative splicing by BMP signaling. Developmental Dynamics 239:2413-2425,

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“…A well-studied example is Sxl, Tra, Tra-2, and several other splicing factors in Drosophila, which regulate a cascade of AS events to control sex determination (Lopez 1998). In mammals, tissue-specific splicing factors include Nova-1/2, PTB/nPTB, Fox-1/2, Muscleblind-like (MBNL) and CELF family proteins, Hu proteins, TIA1/TIAR, and probably many more yet to be characterized (for reviews, see Li et al 2007;David and Manley 2008). The identification of the RNA targets of these factors is critical for …”

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confidence: 99%

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2

Zhang¹,

Zuo²,

Castle³

et al. 2008

Genes Dev.

275

289

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The precise regulation of many alternative splicing (AS) events by specific splicing factors is essential to determine tissue types and developmental stages. However, the molecular basis of tissue-specific AS regulation and the properties of splicing regulatory networks (SRNs) are poorly understood. Here we comprehensively predict the targets of the brain-and muscle-specific splicing factor Fox-1 (A2BP1) and its paralog Fox-2 (RBM9) and systematically define the corresponding SRNs genome-wide. Fox-1/2 are conserved from worm to human, and specifically recognize the RNA element UGCAUG. We integrate Fox-1/2-binding specificity with phylogenetic conservation, splicing microarray data, and additional computational and experimental characterization. We predict thousands of Fox-1/2 targets with conserved binding sites, at a false discovery rate (FDR) of ∼24%, including many validated experimentally, suggesting a surprisingly extensive SRN. The preferred position of the binding sites differs according to AS pattern, and determines either activation or repression of exon recognition by Fox-1/2. Many predicted targets are important for neuromuscular functions, and have been implicated in several genetic diseases. We also identified instances of binding site creation or loss in different vertebrate lineages and human populations, which likely reflect fine-tuning of gene expression regulation during evolution.[Keywords: Tissue-specific alternative splicing; splicing regulatory network; Fox-1/A2BP1; Fox-2/RBM9; UGCAUG; comparative genomics] Supplemental material is available at http://www.genesdev.org.Received June 6, 1007; revised version accepted July 28, 2008.The sequencing of complete genomes revealed that complex metazoans, including mammals, have only slightly more genes than unicellular yeast (International Human Genome Sequencing Consortium 2001). Organismal complexity must have resulted largely from mechanisms for diversifying the expression products, and the temporal and spatial patterns, from a limited set of genes. It is crucial to understand how gene expression is orchestrated to determine developmental stages, specify cell types, and respond to external stimuli (Maniatis and Reed 2002). Alternative splicing (AS), the process for removing introns from pre-mRNA transcripts and joining exons in different combinations, is an essential step of post-transcriptional regulation (Cartegni et al. 2002;Black 2003). In mammals, more than two-thirds of genes are alternatively spliced (Johnson et al. 2003). The choice of exons and splice sites is largely determined by many RNA-binding proteins, or splicing factors, which interact with cis-regulatory elements to activate or repress particular splicing events.Many splicing factors have restricted and dynamic expression patterns, and play important roles in tissue-specific or developmentally regulated splicing of particular transcripts. However, the mechanisms and impact of these AS events remain poorly understood. A well-studied example is Sxl, Tra, Tra-2, and several other s...

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The search for alternative splicing regulators: new approaches offer a path to a splicing code

Cited by 49 publications

References 48 publications

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

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

Identification of downstream targets of the Bone Morphogenetic Protein pathway in the Drosophila nervous system

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2

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