Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 107; no. 27; pp. 12186 - 12191
• Main Authors: McIlwain, David R., Pan, Qun, Reilly, Patrick T., Elia, Andrew J., McCracken, Susan, Wakeham, Andrew C., Itie-Youten, Annick, Blencowe, Benjamin J., Mak, Tak W.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 06.07.2010; National Acad Sciences
• Subjects: Alternative Splicing; Animals; Biological Sciences; Cell lines; Cells, Cultured; Embryo, Mammalian - cytology; Embryo, Mammalian - embryology; Embryo, Mammalian - metabolism; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Embryos; Exons; Female; Gene expression; Gene Expression Profiling; Gene expression regulation; Genes; Genes, Lethal; Genetics; Immunoblotting; Male; Messenger RNA; Mice; Mice, Inbred C57BL; Mice, Inbred Strains; Mice, Knockout; Mutation; Phosphatidylinositol 3-Kinases - genetics; Phosphatidylinositol 3-Kinases - metabolism; Phosphorylation; Protein Serine-Threonine Kinases - genetics; Protein Serine-Threonine Kinases - metabolism; Proteins; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleic acid; RNA; RNA Stability; Rodents; Signal transduction; Splicing
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1007336107

Smg1 is a PI3K-related kinase (PIKK) associated with multiple cellular functions, including DNA damage responses, telomere maintenance, and nonsense-mediated mRNA decay (NMD). NMD degrades transcripts that harbor premature termination codons (PTCs) as a result of events such as mutation or alternative splicing (AS). Recognition of PTCs during NMD requires the action of the Up-stream frameshift protein Upf1, which must first be phosphorylated by Smg1. However, the physiological function of mammalian Smg1 is not known. By using a gene-trap model of Smg1 deficiency, we show that this kinase is essential for mouse embryogenesis such that Smg1 loss is lethal at embryonic day 8.5. High-throughput RNA sequencing (RNA-Seq) of RNA from cells of Smg1-deficient embryos revealed that Smg1 depletion led to pronounced accumulation of PTC-containing splice variant transcripts from approximately 9% of genes predicted to contain AS events capable of eliciting NMD. Among these genes are those involved in splicing itself, as well as genes not previously known to be subject to AS-coupled NMD, including several involved in transcription, intracellular signaling, membrane dynamics, cell death, and metabolism. Our results demonstrate a critical role for Smg1 in early mouse development and link the loss of this NMD factor to major and widespread changes in the mammalian transcriptome.