Deciphering the splicing code. Nature, 465, 53-59

Biomedical Engineering, Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto M5S 3G4, Canada.
Nature (Impact Factor: 41.46). 05/2010; 465(7294):53-9. DOI: 10.1038/nature09000
Source: PubMed

ABSTRACT Alternative splicing has a crucial role in the generation of biological complexity, and its misregulation is often involved in human disease. Here we describe the assembly of a 'splicing code', which uses combinations of hundreds of RNA features to predict tissue-dependent changes in alternative splicing for thousands of exons. The code determines new classes of splicing patterns, identifies distinct regulatory programs in different tissues, and identifies mutation-verified regulatory sequences. Widespread regulatory strategies are revealed, including the use of unexpectedly large combinations of features, the establishment of low exon inclusion levels that are overcome by features in specific tissues, the appearance of features deeper into introns than previously appreciated, and the modulation of splice variant levels by transcript structure characteristics. The code detected a class of exons whose inclusion silences expression in adult tissues by activating nonsense-mediated messenger RNA decay, but whose exclusion promotes expression during embryogenesis. The code facilitates the discovery and detailed characterization of regulated alternative splicing events on a genome-wide scale.

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Available from: Benjamin J Blencowe, Sep 26, 2015
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    • "For instance, while humans have 19.000 genes, Drosophila melanogaster has 14.000 genes and Caenorhabditis elegans has 20.000 genes, the proportion of genes affected by alternative splicing is much higher in humans (95%) [16], than in Drosophila (46%) [17] or C. elegans (25%) [18]. As mentioned above, RNAPII elongates the nascent transcript at an average of 2–3 kb/min, but its speed suffers dramatical changes along the gene. "
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    ABSTRACT: Coupling of transcription and alternative splicing via regulation of the transcriptional elongation rate is a well-studied phenomenon. Template features that act as roadblocks for the progression of RNA polymerase II comprise histone modifications and variants, DNA-interacting proteins and chromatin compaction. These may affect alternative splicing decisions by inducing pauses or decreasing elongation rate that change the time-window for splicing regulatory sequences to be recognized. Herein we discuss the evidence supporting the influence of template structural modifications on transcription and splicing, and provide insights about possible roles of non-B DNA conformations on the regulation of alternative splicing. Copyright © 2015. Published by Elsevier B.V.
    FEBS letters 08/2015; DOI:10.1016/j.febslet.2015.08.002 · 3.17 Impact Factor
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    • " of discriminatory contributions from binding sites for known splicing regulators was the result of not including sufficient numbers of potential binding site se - quences in our RNA feature compendium , we added addi - tional 5mers , 6mers , and 7mers of known binding sites for splicing regulators as well as codon frequencies ( Yeo et al . 2007 ; Barash et al . 2010 ) to increase the RNA feature compen - dium to 826 features . However , training our data sets with the extended RNA fea - ture compendium did not improve the performance of our splicing code ( Sup - plemental Fig . 2 ) , nor did we observe a change in the identity of the RNA features that displayed the highest information gain ( Supple"
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    ABSTRACT: Alternative splicing is a key player in the creation of complex mammalian transcriptomes and its misregulation is associated with many human diseases. Multiple mRNA isoforms are generated from most human genes, a process mediated by the interplay of various RNA signature elements and trans-acting factors that guide spliceosomal assembly and intron removal. Here, we introduce a splicing predictor that evaluates hundreds of RNA features simultaneously to successfully differentiate between exons that are constitutively spliced, exons that undergo alternative 5' or 3' splice-site selection, and alternative cassette-type exons. Surprisingly, the splicing predictor did not feature strong discriminatory contributions from binding sites for known splicing regulators. Rather, the ability of an exon to be involved in one or multiple types of alternative splicing is dictated by its immediate sequence context, mainly driven by the identity of the exon's splice sites, the conservation around them, and its exon/intron architecture. Thus, the splicing behavior of human exons can be reliably predicted based on basic RNA sequence elements. © 2015 Busch and Hertel; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
    RNA 03/2015; 21(5). DOI:10.1261/rna.048769.114 · 4.94 Impact Factor
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    • "Although primarily characterized as a repressive splicing regulator, it can also activate some splice sites and this has been related to differential positions of binding relative to regulated exons (Xue et al, 2009; Llorian et al, 2010). Although PTB can act alone as a regulator (Amir-Ahmady et al, 2005), genome-wide analyses suggest that it cooperates with a number of other proteins as a component of 'tissue spicing codes' (Castle et al, 2008; Wang et al, 2008; Barash et al, 2010; Bland et al, 2010; Llorian et al, 2010). Structure-function analysis has indicated that despite their similar RNA-binding preferences , the four RRMs of PTB show functional diversification (Liu et al, 2002; Robinson & Smith, 2006; Mickleburgh et al, 2014). "
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    ABSTRACT: Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated by PTB. In contrast to other splicing regulators, Matrin3 binds to an extended region within repressed exons and flanking introns with no sharply defined peaks. The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.
    The EMBO Journal 01/2015; 34(5). DOI:10.15252/embj.201489852 · 10.43 Impact Factor
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