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


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.


Available from: Benjamin J Blencowe
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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; 589(22). DOI:10.1016/j.febslet.2015.08.002 · 3.17 Impact Factor
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    • "The diversity in splicing is further increased by the location and nucleotide sequence of premRNA enhancer and silencer motifs that either promote or inhibit splicing by the different regulators. Adding to this complexity, regulating motifs are very common throughout the genome, but are not necessarily functional (Barash et al., 2010; Black, 2003; Fairbrother et al., 2002; Wang et al., 2004; Zhang and Chasin, 2004). "
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    ABSTRACT: Alternative splicing (AS) is one of the major mechanisms to warrant the proteomic and functional diversity of eukaryotes. However, the complex nature of the splicing machinery, its associated splicing regulators and the functional implications of alternatively spliced transcripts is only poorly understood.We investigated here the functional role of the splicing regulator rbfox1 in vivo using the zebrafish as a model system. We find that loss-of rbfox1 leads to progressive cardiac contractile dysfunction and heart failure. By using deep-transcriptome sequencing and quantitative real-time PCR we show that depletion of rbfox1 in zebrafish results in an altered isoform expression of several crucial target genes, such as actn3a and hug.This study underlines that tightly regulated splicing is necessary for unconstrained cardiac function and renders the splicing regulator rbfox1 an interesting target to be investigated in human heart failure and cardiomyopathy. © 2015. Published by The Company of Biologists Ltd.
    Journal of Cell Science 06/2015; 128(16). DOI:10.1242/jcs.166850 · 5.43 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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