Identification of tissue-specific alternative splicing regulatory elements in vivo using a random library approach in C. elegans

2020 ◽  
Author(s):  
Sanjana Bhatnagar
Keyword(s):  
Alternative Splicing ◽  
Regulatory Elements ◽  
Tissue Specific ◽  
C Elegans ◽  
Splicing Regulatory Elements ◽  
Random Library ◽  
Specific Alternative

scholarly journals A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing

2007 ◽  
Vol 35 (14) ◽  
pp. 4845-4857 ◽  
Author(s):  
Debopriya Das ◽  
Tyson A. Clark ◽  
Anthony Schweitzer ◽  
Miki Yamamoto ◽  
Henry Marr ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Regulatory Elements ◽  
Tissue Specific ◽  
Exon Expression ◽  
Specific Alternative

scholarly journals Tissue-specific isoforms of the single C. elegans Ryanodine receptor gene unc-68 control specific functions

PLoS Genetics ◽  
2020 ◽  
Vol 16 (10) ◽  
pp. e1009102
Author(s):  
Filipe Marques ◽  
Saurabh Thapliyal ◽  
Avelino Javer ◽  
Priyanka Shrestha ◽  
André E. X. Brown ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Receptor Gene ◽  
Ryanodine Receptors ◽  
Computer Assisted ◽  
Alternative Promoters ◽  
Tissue Specific ◽  
C Elegans ◽  
Specific Alternative ◽  
And Function ◽  
Different Tissues

Ryanodine receptors (RyR) are essential regulators of cellular calcium homeostasis and signaling. Vertebrate genomes contain multiple RyR gene isoforms, expressed in different tissues and executing different functions. In contrast, invertebrate genomes contain a single RyR-encoding gene and it has long been proposed that different transcripts generated by alternative splicing may diversify their functions. Here, we analyze the expression and function of alternative exons in the C. elegans RyR gene unc-68. We show that specific isoform subsets are created via alternative promoters and via alternative splicing in unc-68 Divergent Region 2 (DR2), which actually corresponds to a region of high sequence variability across vertebrate isoforms. The expression of specific unc-68 alternative exons is enriched in different tissues, such as in body wall muscle, neurons and pharyngeal muscle. In order to infer the function of specific alternative promoters and alternative exons of unc-68, we selectively deleted them by CRISPR/Cas9 genome editing. We evaluated pharyngeal function, as well as locomotor function in swimming and crawling with high-content computer-assisted postural and behavioral analysis. Our data provide a comprehensive map of the pleiotropic impact of isoform-specific mutations and highlight that tissue-specific unc-68 isoforms fulfill distinct functions. As a whole, our work clarifies how the C. elegans single RyR gene unc-68 can fulfill multiple tasks through tissue-specific isoforms, and provide a solid foundation to further develop C. elegans as a model to study RyR channel functions and malfunctions.

scholarly journals The Fox-1 Family and SUP-12 Coordinately Regulate Tissue-Specific Alternative Splicing In Vivo

2007 ◽  
Vol 27 (24) ◽  
pp. 8612-8621 ◽  
Author(s):  
Hidehito Kuroyanagi ◽  
Genta Ohno ◽  
Shohei Mitani ◽  
Masatoshi Hagiwara
Keyword(s):  
Alternative Splicing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Stable Complex ◽  
Tissue Specific ◽  
Specific Alternative

ABSTRACT Many pre-mRNAs are alternatively spliced in a tissue-specific manner in multicellular organisms. The Fox-1 family of RNA-binding proteins regulate alternative splicing by either activating or repressing exon inclusion through specific binding to UGCAUG stretches. However, the precise cellular contexts that determine the action of the Fox-1 family in vivo remain to be elucidated. We have recently demonstrated that ASD-1 and FOX-1, members of the Fox-1 family in Caenorhabditis elegans, regulate tissue-specific alternative splicing of the fibroblast growth factor receptor gene, egl-15, which eventually determines the ligand specificity of the receptor in vivo. Here we report that another RNA-binding protein, SUP-12, coregulates the egl-15 alternative splicing. By screening for mutants defective in the muscle-specific expression of our alternative splicing reporter, we identified the muscle-specific RNA-binding protein SUP-12. We identified juxtaposed conserved stretches as the cis elements responsible for the regulation. The Fox-1 family and the SUP-12 proteins form a stable complex with egl-15 RNA, depending on the cis elements. Furthermore, the asd-1; sup-12 double mutant is defective in sex myoblast migration, phenocopying the isoform-specific egl-15(5A) mutant. These results establish an in vivo model that coordination of the two families of RNA-binding proteins regulates tissue-specific alternative splicing of a specific target gene.

Transfer and tissue-specific accumulation of components in embryos of Caenorhabditis elegans and dolichura: in vivo analysis with a low-cost signal

Development ◽  
1992 ◽  
Vol 114 (2) ◽  
pp. 317-330 ◽  
Author(s):  
O. Bossinger ◽  
E. Schierenberg
Keyword(s):  
Caenorhabditis Elegans ◽  
Low Cost ◽  
Free Living ◽  
Tissue Specific ◽  
C Elegans ◽  
Specific Accumulation ◽  
In Vivo Analysis

The pattern of autofluorescence in the two free-living namatodes Rhabditis dolichura and Caenorhabditis compared. In C. elegans, during later embryogenesis cells develop a typical bluish autofluorescence as illumination, while in Rh. dolichura a strong already present in the unfertilized egg. Using a new,

Tissue-specific alternative splicing of BK channel transcripts in Drosophila

2006 ◽  
Vol 5 (4) ◽  
pp. 329-339 ◽  
Author(s):  
J. Y. Yu ◽  
A. B. Upadhyaya ◽  
N. S. Atkinson
Keyword(s):  
Alternative Splicing ◽  
Bk Channel ◽  
Tissue Specific ◽  
Specific Alternative
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