Minor class splicing shapes the zebrafish transcriptome during development

Markmiller, S., Cloonan, N., Lardelli, R.M., Doggett, K., Keightley, M.C., Boglev, Y., Trotter, A.J., Ng, A.Y., Wilkins, S.J., Verkade, H., Ober, E.A., Field, H.A., Grimmond, S.M., Lieschke, G.J., Stainier, D.Y., and Heath, J.K.
Proceedings of the National Academy of Sciences of the United States of America   111(8): 3062-3067 (Journal)
Registered Authors
Boglev, Yeliz, Doggett, Karen, Field, Holly, Heath, Joan K., Keightley, M. Cristina, Lardelli, Rea, Lieschke, Graham J., Markmiller, Sebastian, Ng, Annie, Ober, Elke, Stainier, Didier, Trotter, Andrew, Verkade, Heather, Wilkins, Simon
GEO:GSE53758, GEO:GSE53934, GEO:GSE53935
MeSH Terms
  • Animals
  • Base Sequence
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental/genetics
  • Gene Expression Regulation, Developmental/physiology*
  • Intestines/abnormalities
  • Liver/abnormalities
  • Microarray Analysis
  • Molecular Sequence Data
  • Pancreas/abnormalities
  • Point Mutation/genetics
  • Protein Conformation*
  • RNA Splicing/genetics
  • RNA Splicing/physiology*
  • RNA, Small Nuclear/chemistry*
  • RNA-Binding Proteins/genetics*
  • RNA-Binding Proteins/metabolism
  • Real-Time Polymerase Chain Reaction
  • Sequence Analysis, RNA
  • Spliceosomes/genetics
  • Spliceosomes/metabolism*
  • Zebrafish/genetics*
  • Zebrafish/growth & development
  • Zebrafish Proteins/genetics*
  • Zebrafish Proteins/metabolism
24516132 Full text @ Proc. Natl. Acad. Sci. USA

Minor class or U12-type splicing is a highly conserved process required to remove a minute fraction of introns from human pre-mRNAs. Defects in this splicing pathway have recently been linked to human disease, including a severe developmental disorder encompassing brain and skeletal abnormalities known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating gene expression, the impact of impaired U12-type splicing on the transcriptome is unknown. Here, we describe a unique zebrafish mutant, caliban (clbn), with arrested development of the digestive organs caused by an ethylnitrosourea-induced recessive lethal point mutation in the rnpc3 [RNA-binding region (RNP1, RRM) containing 3] gene. rnpc3 encodes the zebrafish ortholog of human RNPC3, also known as the U11/U12 di-snRNP 65-kDa protein, a unique component of the U12-type spliceosome. The biochemical impact of the mutation in clbn is the formation of aberrant U11- and U12-containing small nuclear ribonucleoproteins that impair the efficiency of U12-type splicing. Using RNA sequencing and microarrays, we show that multiple genes involved in various steps of mRNA processing, including transcription, splicing, and nuclear export are disrupted in clbn, either through intron retention or differential gene expression. Thus, clbn provides a useful and specific model of aberrant U12-type splicing in vivo. Analysis of its transcriptome reveals efficient mRNA processing as a critical process for the growth and proliferation of cells during vertebrate development.

Genes / Markers
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Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Engineered Foreign Genes