scholarly journals Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome

2019 ◽  
Author(s):  
Marina Reixachs-Solé ◽  
Jorge Ruiz-Orera ◽  
M Mar Albà ◽  
Eduardo Eyras
Keyword(s):  
Alternative Splicing ◽  
Protein Production ◽  
Cellular Mechanism ◽  
Ribosome Profiling ◽  
Differential Analysis ◽  
Differential Splicing ◽  
Transcript Isoforms ◽  
Individual Transcript ◽  
Open Question ◽  
Human And Mouse

AbstractThe differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing), a new pipeline for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (Ribosome profiling). We found evidence of translation for 40-50% of the expressed transcript isoforms in human and mouse, with 53% of the expressed genes having more than one translated isoform in human, 33% in mouse. Differential analysis revealed that about 40% of the splicing changes at RNA level were concordant with changes in translation, with 21.7% of changes at RNA level and 17.8% at translation level conserved between human and mouse. Furthermore, orthologous cassette exons preserving the directionality of the change were conserved between human and mouse and enriched in microexons in a comparison between glia and glioma. ORQAS leverages ribosome profiling to uncover a widespread and evolutionary conserved impact of differential splicing on the translation of isoforms and, in particular, of microexon-containing isoforms. ORQAS is available at https://github.com/comprna/orqas

scholarly journals A survey of computational methods in transcriptome-wide alternative splicing analysis

2015 ◽  
Vol 6 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Jianbo Wang ◽  
Zhenqing Ye ◽  
Tim H.-M. Huang ◽  
Huidong Shi ◽  
Victor Jin
Keyword(s):  
Alternative Splicing ◽  
Experimental Validation ◽  
Gene Diversity ◽  
Exon Skipping ◽  
Differential Splicing ◽  
Sequencing Data ◽  
Future Directions ◽  
Specific Analysis ◽  
Software Implementations ◽  
Expected Outcomes

AbstractAlternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.

scholarly journals Tunable protein synthesis by transcript isoforms in human cells

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Stephen N Floor ◽  
Jennifer A Doudna
Keyword(s):  
Translational Control ◽  
Protein Production ◽  
Dynamic Range ◽  
Human Cells ◽  
Untranslated Regions ◽  
Specific Expression ◽  
Transcript Isoforms ◽  
Protein Levels ◽  
Eukaryotic Genes ◽  
Control Protein

Eukaryotic genes generate multiple RNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). Analysis of these data revealed regulatory features that control ribosome occupancy and translational output of each transcript isoform. We extracted a panel of 5′ and 3′ untranslated regions that control protein production from an unrelated gene in cells over a 100-fold range. Select 5′ untranslated regions exert robust translational control between cell lines, while 3′ untranslated regions can confer cell type-specific expression. These results expose the large dynamic range of transcript-isoform-specific translational control, identify isoform-specific sequences that control protein output in human cells, and demonstrate that transcript isoform diversity must be considered when relating RNA and protein levels.

scholarly journals Single-cell Differential Splicing Analysis Reveals High Heterogeneity of Liver Tumor-infiltrating T Cells

2020 ◽  
Author(s):  
Shang Liu ◽  
Biaofeng Zhou ◽  
Liang Wu ◽  
Yan Sun ◽  
Jie Chen ◽  
...  
Keyword(s):  
T Cells ◽  
Alternative Splicing ◽  
T Cell ◽  
Single Cell ◽  
Regulatory Factor ◽  
Differential Splicing ◽  
Cell Level ◽  
Comprehensive Investigation ◽  
Cancer Initiation ◽  
Cell Groups

Abstract Recent advances in single-cell RNA sequencing (scRNA-seq) have improved our understanding of the association between tumor-infiltrating lymphocyte (TILs) heterogeneity and cancer initiation and progression. However, studies investigating alternative splicing (AS) as an important regulatory factor of heterogeneity remain limited. Here, we developed a new computational tool, DESJ-detection, which accurately detects differentially expressed splicing junctions (DESJs) between cell groups at the single-cell level. We analyzed 5,063 T cells of hepatocellular carcinoma (HCC) and identified 1,176 DESJs across 11 T cell subtypes. Interestingly, DESJs were enriched in UTRs, and have putative effects on heterogeneity. Cell subtypes with a similar function closely clustered together at the AS level. Meanwhile, we identified two novel cell states, pre-exhaustion and pre-activation with the isoform markers CD103-201 and ARHGAP15-205. In summary, we present a comprehensive investigation of alternative splicing differences, which provided novel insights into T cell heterogeneity and can be applied to other full-length scRNA-seq datasets.

scholarly journals Alternative Splicing of Transcription Factors' Genes: Beyond the Increase of Proteome Diversity

2009 ◽  
Vol 2009 ◽  
pp. 1-6 ◽  
Author(s):  
David Talavera ◽  
Modesto Orozco ◽  
Xavier de la Cruz
Keyword(s):  
Transcription Factors ◽  
Alternative Splicing ◽  
Expression Patterns ◽  
Developmental Changes ◽  
Functional Families ◽  
Transcription Regulators ◽  
Alternatively Spliced ◽  
The Impact ◽  
Human And Mouse

Functional modification of transcription regulators may lead to developmental changes and phenotypical differences between species. In this work, we study the influence of alternative splicing on transcription factors in human and mouse. Our results show that the impact of alternative splicing on transcription factors is similar in both species, meaning that the ways to increase variability should also be similar. However, when looking at the expression patterns of transcription factors, we observe that they tend to diverge regardless of the role of alternative splicing. Finally, we hypothesise that transcription regulation of alternatively spliced transcription factors could play an important role in the phenotypical differences between species, without discarding other phenomena or functional families.

scholarly journals CELF2 regulates the species-specific alternative splicing of TREM2

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Motoaki Yanaizu ◽  
Chika Washizu ◽  
Nobuyuki Nukina ◽  
Jun-ichi Satoh ◽  
Yoshihiro Kino
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Full Length ◽  
Splicing Regulation ◽  
Nonsense Mediated Mrna Decay ◽  
Specific Alternative ◽  
Species Specific ◽  
Human And Mouse ◽  
Paralogous Proteins

Abstract Genetic variations of TREM2 have been implicated as a risk factor of Alzheimer’s disease (AD). Recent studies suggest that the loss of TREM2 function compromises microglial responses to the accumulation of amyloid beta. Previously, we found that exon 3 of TREM2 is an alternative exon whose skipping leads to a reduction in full-length TREM2 protein by inducing nonsense-mediated mRNA decay. Here, we aimed to identify factors regulating TREM2 splicing. Using a panel of RNA-binding proteins, we found that exon 3 skipping of TREM2 was promoted by two paralogous proteins, CELF1 and CELF2, which were both linked previously with risk loci of AD. Although the overexpression of both CELF1 and CELF2 enhanced exon 3 skipping, only CELF2 reduced the expression of full-length TREM2 protein. Notably, the TREM2 ortholog in the green monkey, but not in the mouse, showed alternative splicing of exon 3 like human TREM2. Similarly, splicing regulation of exon 3 by CELF1/2 was found to be common to humans and monkeys. Using chimeric minigenes of human and mouse TREM2, we mapped a CELF-responsive sequence within intron 3 of human TREM2. Collectively, our results revealed a novel regulatory factor of TREM2 expression and highlighted a species-dependent difference of its regulation.

scholarly journals AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse

2009 ◽  
Vol 37 (Database) ◽  
pp. D305-D309 ◽  
Author(s):  
M. Shionyu ◽  
A. Yamaguchi ◽  
K. Shinoda ◽  
K.-i. Takahashi ◽  
M. Go
Keyword(s):  
Alternative Splicing ◽  
Protein Structure ◽  
Structure Interaction ◽  
Human And Mouse

scholarly journals Structural Organization of the Human and Mouse Laminin β2 Chain Genes, and Alternative Splicing at the 5′ End of the Human Transcript

1996 ◽  
Vol 271 (23) ◽  
pp. 13407-13416 ◽  
Author(s):  
Marian E. Durkin ◽  
Medha Gautam ◽  
Frosty Loechel ◽  
Joshua R. Sanes ◽  
John P. Merlie ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Structural Organization ◽  
Human Transcript ◽  
Human And Mouse ◽  
Laminin Β2

scholarly journals TISA: Tissue-specific Alternative Splicing in Human and Mouse Genes

DNA Research ◽  
2006 ◽  
Vol 13 (5) ◽  
pp. 229-243 ◽  
Author(s):  
Seung-Jae Noh ◽  
Kyooyeol Lee ◽  
Hyojung Paik ◽  
Cheol-Goo Hur
Keyword(s):  
Alternative Splicing ◽  
Tissue Specific ◽  
Specific Alternative ◽  
Human And Mouse
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