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An intron is any sequence within a gene removed by RNA splicing.
Intron sequences joined together in the final RNA, after splicing, are called exons.
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Found gene defect causes developmental errors
Melbourne researchers have made a major step in understanding changes in the cellular process called minor class splicing. The defect may cause a severe developmental disease known as Taybi-Linder syndrome.
Using zebrafish, a popular laboratory model for studying development, researchers have discovered that the protein Rnpc3 is critical to the growth of many organs. Rnpc3 regulates protein production through a process called minor class messenger RNA splicing.
Messenger RNA is a molecule required to convert gene blueprints coded in DNA into proteins. Using a 'cut and paste' process, RNA cuts unwanted sequences — called introns — out of messenger RNA, and pastes the remaining pieces back together again.Without splicing these unwanted sequences, proteins cannot be made correctly from genes.
Joan Heath, Ludwig Member and Associate Professor at the Walter and Eliza Hall Institute, and Dr Sebastian Markmiller, University of California, San Diego, found that the protein Rnpc3 is required for the rapid growth of organs, including the intestine, liver, pancreas and eye, during zebrafish development. Their findings are published in the journal Proceedings of the National Academy of Sciences.
Associate Professor Heath said the discovery was important because it helped shed light on how defects in minor class splicing cause a severe human developmental disorder known as Taybi-Linder syndrome.
"Altogether there are about 200,000 introns in the genome [all the genetic material in one individual]. Most introns are removed through a process known as major class splicing.
"Minor class splicing is more rare and removes only a few hundred introns. Why minor class splicing exists at all, and how important it is, has eluded geneticists for more than two decades. We have now discovered that minor class splicing is critical to the expression of genes that regulate gene expression.
"Defects in minor class splicing effects which genes are switched on — particularly critical in development when rapid changes in gene expression and protein production are required.
"In the long-run, we anticipate our research will show that minor class splicing contributes to other diseases currently not fully understood,"
Joan Heath, Associate Professor and Ludwig Member, Walter and Eliza Hall Institute
The accurate removal of introns by pre-mRNA splicing is a critical step in proper gene expression. Most eukaryotic genomes, from plant to human, contain a tiny subset of “minor class” introns with unique sequence elements that require their own splicing machinery. The significance of this second splicing pathway has intrigued RNA biologists for two decades, but its biological relevance was recently underscored when defects in the process were firmly linked to human disease. Here, we use a novel zebrafish mutant with defective minor class splicing to investigate how this pathway shapes the transcriptome during vertebrate development. We link its pleiotropic phenotype to widespread changes in gene expression that disrupt essential cellular pathways, including mRNA processing.
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.
1Present address: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla CA 92093.
2N.C. and R.M.L. contributed equally to this work.
3Present address: QIMR Berghofer Medical Research Institute, Genomic Biology Laboratory, Herston, QLD 4006, Australia.
4Present address: Division of Biology, University of California, San Diego, La Jolla, CA 92093.
5Present address: Institute of Medical Biology, Agency for Science, Technology and Research (A-STAR), Singapore 138648.
6Present address: The Danish Stem Cell Centre, University of Copenhagen, 2200 Copenhagen, Denmark.
7Present address: Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany.
8To whom correspondance should be addressed. E-mail: email@example.com.
Author contributions: S.M., R.M.L., and J.K.H. designed research; S.M., R.M.L., K.D., M.-C.K., Y.B., A.J.T., A.Y.N., S.J.W., and H.V. performed research; N.C., H.V., E.A.O., H.A.F., S.M.G., and D.Y.R.S. contributed new reagents/analytic tools; S.M., N.C., R.M.L., K.D., M.-C.K., Y.B., A.J.T., A.Y.N., S.J.W., G.J.L., and J.K.H. analyzed data; and S.M. and J.K.H. wrote the paper.
The authors declare no conflict of interest.
*This Direct Submission article had a prearranged editor.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE53935).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1305536111/-/DCSupplemental.
Freely available online through the PNAS open access option.
The research was supported by the Australian National Health and Medical Research Council, the Boehringer Ingelheim Foundation, Ludwig Cancer Research and the Victorian Government.