title: A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii.
abstract: Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoured in this phylum. We investigated the mechanism of alternative splicing in Toxoplasma gondii, and have identified and localized TgSR3, a homologue of ASF/SF2 (alternative-splicing factor/splicing factor 2, a serine-arginine-rich, or SR protein) to a subnuclear compartment. In addition, we conditionally overexpressed this protein, which was deleterious to growth. qRT-PCR was used to confirm perturbation of splicing in a known alternatively-spliced gene. We performed high-throughput RNA-seq to determine the extent of splicing modulated by this protein. Current RNA-seq algorithms are poorly suited to compact parasite genomes, and hence we complemented existing tools by writing a new program, GeneGuillotine, that addresses this deficiency by segregating overlapping reads into distinct genes. In order to identify the extent of alternative splicing, we released another program, JunctionJuror, that detects changes in intron junctions. Using this program, we identified about 2000 genes that were constitutively alternatively spliced in T. gondii. Overexpressing the splice regulator TgSR3 perturbed alternative splicing in over 1000 genes.
authors: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors: Lee M
authors: LM
authors: Yeoh
authors: School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors: Christopher D
authors: CD
authors: Goodman
authors: Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia.
authors: Nathan E
authors: NE
authors: Hall
authors: Research School of Biology, The Australian National University, Acton, ACT 2601, Australia.
authors: Giel G
authors: GG
authors: van Dooren
authors: School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors: Geoffrey I
authors: GI
authors: McFadden
authors: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia saralph@unimelb.edu.au.
authors: Stuart A
authors: SA
authors: Ralph
mesh_terms: D017398:Alternative Splicing; D022003:Cell Nucleus Structures / Q000737:chemistry; D015870:Gene Expression; D009687:Nuclear Proteins / Q000032:analysis / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D010963:Plasmodium falciparum / Q000235:genetics; D015800:Protozoan Proteins / Q000032:analysis / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000032:analysis / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D000068103:Serine-Arginine Splicing Factors; D012984:Software; D014122:Toxoplasma / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D009687:Nuclear Proteins; D015800:Protozoan Proteins; D016601:RNA-Binding Proteins; D000068103:Serine-Arginine Splicing Factors