PUBLICATION
Experimental approaches to studying the nature and impact of splicing variation in zebrafish
- Authors
- Keightley, M.C., Markmiller, S., Love, C.G., Rasko, J.E., Lieschke, G.J., Heath, J.K.
- ID
- ZDB-PUB-160725-23
- Date
- 2016
- Source
- Methods in cell biology 135: 259-88 (Chapter)
- Registered Authors
- Heath, Joan K., Keightley, M. Cristina, Lieschke, Graham J., Love, Chris, Markmiller, Sebastian
- Keywords
- Alternative splicing, Disease models, Intron retention, RNAseq, Spliceopathy, Spliceosome, Splicing, Zebrafish, prpf8, rnpc3
- MeSH Terms
-
- Alternative Splicing/genetics*
- Animals
- Gene Expression Profiling/methods*
- Mutation/genetics
- Phenotype
- RNA Precursors/genetics
- RNA-Binding Proteins/genetics
- Spliceosomes/genetics*
- Spliceosomes/ultrastructure
- Transcriptome/genetics*
- Zebrafish/genetics
- Zebrafish Proteins/genetics
- PubMed
- 27443930 Full text @ Meth. Cell. Biol.
Citation
Keightley, M.C., Markmiller, S., Love, C.G., Rasko, J.E., Lieschke, G.J., Heath, J.K. (2016) Experimental approaches to studying the nature and impact of splicing variation in zebrafish. Methods in cell biology. 135:259-88.
Abstract
From a fixed number of genes carried in all cells, organisms create considerable diversity in cellular phenotype through differential regulation of gene expression. One prevalent source of transcriptome diversity is alternative pre-mRNA splicing, which is manifested in many different forms. Zebrafish models of splicing dysfunction due to mutated spliceosome components provide opportunity to link biochemical analyses of spliceosome structure and function with whole organism phenotypic outcomes. Drawing from experience with two zebrafish mutants: cephalophŏnus (a prpf8 mutant, isolated for defects in granulopoiesis) and caliban (a rnpc3 mutant, isolated for defects in digestive organ development), we describe the use of glycerol gradient sedimentation and native gel electrophoresis to resolve components of aberrant splicing complexes. We also describe how RNAseq can be employed to examine relatively rare alternative splicing events including intron retention. Such experimental approaches in zebrafish can promote understanding of how splicing variation and dysfunction contribute to phenotypic diversity and disease pathogenesis.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping