1. An extended catalogue of tandem alternative splice sites in human tissue transcriptomes
- Author
-
Dmitri D. Pervouchine, Stepan Denisov, Alexey Mironov, Alexander Gress, Olga V. Kalinina, and HIPS, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Universitätscampus E8.1 66123 Saarbrücken, Germany.
- Subjects
Natural selection ,RNA-binding protein ,RNA-binding proteins ,Biochemistry ,Transcriptome ,Gene expression ,Human proteome project ,Natural Selection ,Macromolecular Structure Analysis ,Biology (General) ,Ecology ,Genome project ,PTBP1 ,Genomics ,splice site ,Nucleic acids ,Computational Theory and Mathematics ,Modeling and Simulation ,RNA splicing ,Research Article ,Protein Structure ,Evolutionary Processes ,splicing noise ,QH301-705.5 ,Computational biology ,Biology ,Human Genomics ,Cellular and Molecular Neuroscience ,Genetics ,Humans ,Short linear motif ,splice ,RNA, Messenger ,Indel ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Alternative splicing ,Biology and Life Sciences ,Computational Biology ,Proteins ,Genome Analysis ,Genome Annotation ,Alternative Splicing ,RNA processing ,RNA ,Structural Genomics - Abstract
Tandem alternative splice sites (TASS) is a special class of alternative splicing events that are characterized by a close tandem arrangement of splice sites. Most TASS lack functional characterization and are believed to arise from splicing noise. Based on the RNA-seq data from the Genotype Tissue Expression project, we present an extended catalogue of TASS in healthy human tissues and analyze their tissue-specific expression. The expression of TASS is usually dominated by one major splice site (maSS), while the expression of minor splice sites (miSS) is at least an order of magnitude lower. Among 46k miSS with sufficient read support, 9k (20%) are significantly expressed above the expected noise level, and among them 2.5k are expressed tissue-specifically. We found significant correlations between tissue-specific expression of RNA-binding proteins (RBP), tissue-specific expression of miSS, and miSS response to RBP inactivation by shRNA. In combination with RBP profiling by eCLIP, this allowed prediction of novel cases of tissue-specific splicing regulation including a miSS in QKI mRNA that is likely regulated by PTBP1. The analysis of human primary cell transcriptomes suggested that both tissue-specific and cell-type-specific factors contribute to the regulation of miSS expression. More than 20% of tissue-specific miSS affect structured protein regions and may adjust protein-protein interactions or modify the stability of the protein core. The significantly expressed miSS evolve under the same selection pressure as maSS, while other miSS lack signatures of evolutionary selection and conservation. Using mixture models, we estimated that not more than 15% of maSS and not more than 54% of tissue-specific miSS are noisy, while the proportion of noisy splice sites among non-significantly expressed miSS is above 63%., Author summary Pre-mRNA splicing is an important step in the processing of the genomic information during gene expression. During splicing, introns are excised from a gene transcript, and the remaining exons are ligated. Our work concerns one its particular subtype, which involves the so-called tandem alternative splice sites, a group of closely located exon borders that are used alternatively. We analyzed RNA-seq measurements of gene expression provided by the Genotype-Tissue Expression (GTEx) project, the largest to-date collection of such measurements in healthy human tissues, and constructed a detailed catalogue of tandem alternative splice sites. Within this catalogue, we characterized patterns of tissue-specific expression, regulation, impact on protein structure, and evolutionary selection acting on tandem alternative splice sites. In a number of genes, we predicted regulatory mechanisms that could be responsible for choosing one of many tandem alternative splice sites. The results of this study provide an invaluable resource for molecular biologists studying alternative splicing.
- Published
- 2021