iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Wang, Zheng; Kayikci, Melis; Briese, Michael; Zarnack, Kathi; Luscombe, Nicholas M.; Rot, Gregor; Zupan, Blaž; Curk, Tomaž; Ule, Jernej

doi:10.1371/journal.pbio.1000530

Cited by 214 publications

(293 citation statements)

References 47 publications

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“…To the best of our knowledge, FasterDB is the first database integrating large-scale data sets focused on splicing, including CLIP-seq and splicing-sensitive microarray data sets (Hung et al 2008;Warzecha et al 2009b;Xiao et al 2009Xiao et al , 2012Xue et al 2009;Yeo et al 2009;Katz et al 2010;Llorian et al 2010;Wang et al 2010;Grellscheid et al 2011;Lebedeva et al 2011;Mukherjee et al 2011;Huelga et al 2012;Lagier-Tourenne et al 2012;Zarnack et al 2013). Our next goal will be to include other data sets, such as RNA-seq data sets.…”

Section: Discussionmentioning

confidence: 99%

Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin

et al. 2013

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Alternative splicing is the main mechanism of increasing the proteome diversity coded by a limited number of genes. It is well established that different tissues or organs express different splicing variants. However, organs are composed of common major cell types, including fibroblasts, epithelial, and endothelial cells. By analyzing large-scale data sets generated by The ENCODE Project Consortium and after extensive RT-PCR validation, we demonstrate that each of the three major cell types expresses a specific splicing program independently of its organ origin. Furthermore, by analyzing splicing factor expression across samples, publicly available splicing factor binding site data sets (CLIP-seq), and exon array data sets after splicing factor depletion, we identified several splicing factors, including ESRP1 and 2, MBNL1, NOVA1, PTBP1, and RBFOX2, that contribute to establishing these cell type-specific splicing programs. All of the analyzed data sets are freely available in a user-friendly web interface named FasterDB, which describes all known splicing variants of human and mouse genes and their splicing patterns across several dozens of normal and cancer cells as well as across tissues. Information regarding splicing factors that potentially contribute to individual exon regulation is also provided via a dedicated CLIP-seq and exon array data visualization interface. To the best of our knowledge, FasterDB is the first database integrating such a variety of large-scale data sets to enable functional genomics analyses at exon-level resolution.[Supplemental material is available for this article.]Human genes are an assemblage of exons that can be differentially selected during splicing. Alternative splicing, which can produce splicing variants with different exonic content from a single gene, is the rule rather than an exception, as 95% of human genes generate several splicing variants (Kim et al. 2008;Hallegger et al. 2010;Kalsotra and Cooper 2011;Blencowe 2012;Kelemen et al. 2013). Alternative splicing relies on the combinatory action of splicing factors (e.g., SR and hnRNP proteins) that bind to exonic or intronic splicing regulatory sequences to either strengthen or inhibit splice site recognition by the splicing machinery, therefore enhancing or repressing the inclusion of alternative exons (Barash et al. 2010;Goren et al. 2010;Witten and Ule 2011). Similarly to how transcription factors control transcriptional programs by directing the expression of gene networks, splicing factors control splicing programs by regulating alternative splicing of co-regulated exons (Hartmann and Valcarcel 2009;Barash et al.

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Section: Discussionmentioning

confidence: 99%

Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin

et al. 2013

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“…Following UV cross-linking and RNAase digestion, the RBP-RNA complex is purified by a two-step affinity purification. RNA from these complexes is then deep sequenced (Wang et al, 2010b). Allows purification of RBP-RNA complexes.…”

Section: Pars Sequencingmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

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Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

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“…Biological replicates were highly reproducible (Supplemental Table S2), and pooled reads yielded between 1.8 million and 14 million unique cross-link events per data set (Supplemental Table S3). Significant cross-link events (false discovery rate [FDR] < 0.05) were extracted as previously described (Yeo et al 2009;König et al 2010;Wang et al 2010), yielding a total of 125,474-214,306 binding sites per protein. Each protein cross-linked to thousands of exons and bound similar numbers of target mRNAs across the range of mRNA expression levels (Supplemental Fig.…”

Section: Sr Proteins and Nxf1 Cross-link To Spliced Mrnas And Reside mentioning

confidence: 99%

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

et al. 2016

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Nuclear export factor 1 (NXF1) exports mRNA to the cytoplasm after recruitment to mRNA by specific adaptor proteins. How and why cells use numerous different export adaptors is poorly understood. Here we critically evaluate members of the SR protein family (SRSF1-7) for their potential to act as NXF1 adaptors that couple pre-mRNA processing to mRNA export. Consistent with this proposal, >1000 endogenous mRNAs required individual SR proteins for nuclear export in vivo. To address the mechanism, transcriptome-wide RNA-binding profiles of NXF1 and SRSF1-7 were determined in parallel by individual-nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP). Quantitative comparisons of RNA-binding sites showed that NXF1 and SR proteins bind mRNA targets at adjacent sites, indicative of cobinding. SRSF3 emerged as the most potent NXF1 adaptor, conferring sequence specificity to RNA binding by NXF1 in last exons. Interestingly, SRSF3 and SRSF7 were shown to bind different sites in last exons and regulate 3 ′ untranslated region length in an opposing manner. Both SRSF3 and SRSF7 promoted NXF1 recruitment to mRNA. Thus, SRSF3 and SRSF7 couple alternative splicing and polyadenylation to NXF1-mediated mRNA export, thereby controlling the cytoplasmic abundance of transcripts with alternative 3 ′ ends.

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iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Abstract: Transcriptome-wide analysis of protein-RNA interactions predicts the dual splicing effects of TIA proteins, showing that their local enhancing function is associated with diverse distal splicing silencing effects.

Cited by 214 publications

References 47 publications

Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin

Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin

Complexity of the Alternative Splicing Landscape in Plants

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

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