Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression

Abstract

Messenger RNAs containing premature stop codons are generally targeted for degradation through nonsense-mediated mRNA decay (NMD). This mechanism degrades aberrant transcripts derived from mutant genes containing nonsense or frameshift mutations. Wild-type genes also give rise to transcripts targeted by NMD. For example, some wild-type genes give rise to alternatively spliced transcripts that are targeted for decay by NMD. In Caenorhabditis elegans, the ribosomal protein (rp) L12 gene generates a nonsense codon-bearing alternatively spliced transcript that is induced in an autoregulatory manner by the rpL12 protein. By pharmacologically blocking the NMD pathway, we identified alternatively spliced mRNA transcripts derived from the human rpL3 and rpL12 genes that are natural targets of NMD. The deduced protein sequence of these alternatively spliced transcripts suggests that they are unlikely to encode functional ribosomal proteins. Overexpression of rpL3 increased the level of the alternatively spliced rpL3 mRNA and decreased the normally expressed rpL3. This indicates that rpL3 regulates its own production by a negative feedback loop and suggests the possibility that NMD participates in this regulatory loop by degrading the non-functional alternatively spliced transcript.

Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability

“…These results correlate with previous observations, referred to as feedback regulation 32 or autoregulation. 33 Finally, RNA-seq tags were piled up on the last exon of the RPL12 transcript variant 2, a known NMD target, 50 in response to UPF1 knockdown, indicating that the splicing variant recognized by NMD had escaped from degradation in response to UPF1 depletion (Fig. 2).…”

The Coupling of Alternative Splicing and Nonsense-Mediated mRNA Decay

“…64 More recently, NMD-target isoforms of the human ribosomal protein genes rpL3 and rpL12 were identified and the unproductive splicing of rpL3 was shown to be autoregulated by rpL3 protein in a negative feedback loop. 99 RUST thus seems to play a similar role in the regulation of ribosomal proteins in species from yeast to human.…”

Introns in UTRs: Why we should stop ignoring them

“…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].…”