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

Abstract

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 Upstream 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.gene trap | Smg-1

Introns in UTRs: Why we should stop ignoring them

“…Also enriched amongst NMD targets are mRNAs involved in development and differentiation [45,46]. Consistent with this, NMD-deficient mice fail to .…”

“…In addition to facilitating elimination of the nonfunctional mRNAs described above, significant evidence exists that some 3UIs serve to modulate normal gene expression [40,[43][44][45][46][47][48][49]. Three classes of 3UI-containing mRNAs are both functional and subject to NMD (Fig.…”

“…The most dramatic functional enrichment among NMD-affected transcripts is for those encoding RNA-binding proteins [45,66]. Within this class of genes, exons that introduce stop codons upstream of introns are extremely wellconserved [44,67].…”

“…That is, as an RNA binding protein increases in abundance, it increasingly binds its own pre-mRNA and facilitates production of a 3UI-containing form subject to NMD, thereby maintaining protein homeostasis [44,67,68]. Proteins undergoing this type of regulation include ribosomal proteins [42,[69][70][71], core spliceosomal proteins [66,72] and alternative splicing regulators such as hnRNP and SR proteins [45,67]. In fact, every one of the 11 human SR proteins has a 3UI isoform and regulates its own production by AS-NMD [67].…”

“…Insights & Perspectives ..... complete embryogenesis, with the most prominent defects observed in heart, brain, and hematopoietic development [45,47,73,74]. The neural development program incorporates NMD in at least two important ways, both with widespread effects.…”