Nonsense-associated alternative splicing of T-cell receptor beta genes: no evidence for frame dependence

Identification of diagnostic and prognostic genetic alterations in uveal melanoma using RNA sequencing

Uveal melanoma is a lethal intraocular tumour, in which the presence of various genetic alterations correlates with the risk of metastatic dissemination and survival. Here, we tested the detectability of all key mutations and chromosomal changes from RNA sequencing data in 80 primary uveal melanomas studied by The Cancer Genome Atlas (TCGA) initiative, and in five prospective cases. Whereas unsupervised gene expression profiling strongly indicated the presence of chromosome 3 alterations, it was not reliable in identifying other alterations. Though, the presence of both chromosome 3 and 8q copy number alterations could be successfully inferred from expressed allelic imbalances of heterozygous common single nucleotide polymorphisms. Most mutations were adequately recognised in the RNA by their nucleotide changes (all genes), alternative splicing around the mutation (BAP1) and transcriptome-wide aberrant splicing (SF3B1). Notably, in the TCGA cohort we detected previously unreported mutations in BAP1 (n = 3) and EIF1AX (n = 5), that were missed by the original DNA sequencing. In our prospective cohort, all genetic alterations were successfully identified by combining the described approaches. In conclusion, a transcriptional analysis presents insights into the expressed tumour genotype and its phenotypic consequences and may augment or even substitute DNA-based approaches, with potential applicability in research and clinical practice.

Escaping from CRISPR-Cas-mediated knockout: the facts, mechanisms, and applications

Clustered regularly interspaced short palindromic repeats and associated Cas protein (CRISPR-Cas), a powerful genome editing tool, has revolutionized gene function investigation and exhibits huge potential for clinical applications. CRISPR-Cas-mediated gene knockout has already become a routine method in research laboratories. However, in the last few years, accumulating evidences have demonstrated that genes knocked out by CRISPR-Cas may not be truly silenced. Functional residual proteins could be generated in such knockout organisms to compensate the putative loss of function, termed herein knockout escaping. In line with this, several CRISPR-Cas-mediated knockout screenings have discovered much less abnormal phenotypes than expected. How does knockout escaping happen and how often does it happen have not been systematically reviewed yet. Without knowing this, knockout results could easily be misinterpreted. In this review, we summarize these evidences and propose two main mechanisms allowing knockout escaping. To avoid the confusion caused by knockout escaping, several strategies are discussed as well as their advantages and disadvantages. On the other hand, knockout escaping also provides convenient tools for studying essential genes and treating monogenic disorders such as Duchenne muscular dystrophy, which are discussed in the end.

Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption

Transcripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exonic cis motifs, such as exonic splice enhancers (ESEs), are disrupted by nonsense mutations. We employ genome-wide transcriptomic and k-mer enrichment methods to scrutinize this model. First, we show that ESEs are prone to disruptive nonsense mutations owing to their purine richness and paucity of TGA, TAA and TAG. The motif model correctly predicts that NAS rates should be low (we estimate 5–30%) and approximately in line with estimates for the rate at which random point mutations disrupt splicing (8–20%). Further, we find that, as expected, NAS-associated PTCs are predictable from nucleotide-based machine learning approaches to predict splice disruption and, at least for pathogenic variants, are enriched in ESEs. Finally, we find that both in and out of frame mutations to TAA, TGA or TAG are associated with exon skipping. While a higher relative frequency of such skip-inducing mutations in-frame than out of frame lends some credence to the scanning model, these results reinforce the importance of considering splice motif modulation to understand the etiology of PTC-associated disease.

Readthrough of stop codons under limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay

To gain insight into the mechanistic link between translation termination and nonsense-mediated mRNA decay (NMD), we depleted the ribosome recycling factor ABCE1 in human cells, resulting in an upregulation of NMD-sensitive mRNAs. Suppression of NMD on these mRNAs occurs prior to their SMG6-mediated endonucleolytic cleavage. ABCE1 depletion caused ribosome stalling at termination codons (TCs) and increased ribosome occupancy in 3′ UTRs, implying enhanced TC readthrough. ABCE1 knockdown indeed increased the rate of readthrough and continuation of translation in different reading frames, providing a possible explanation for the observed NMD inhibition, since enhanced readthrough displaces NMD activating proteins from the 3′ UTR. Our results indicate that stalling at TCs triggers ribosome collisions and activates ribosome quality control. Collectively, we show that improper translation termination can lead to readthrough of the TC, presumably due to ribosome collisions pushing the stalled ribosomes into the 3′ UTR, where it can resume translation in-frame as well as out-of-frame.

Mechanisms and Regulation of Nonsense-Mediated mRNA Decay and Nonsense-Associated Altered Splicing in Lymphocytes

The presence of premature termination codons (PTCs) in transcripts is dangerous for the cell as they encode potentially deleterious truncated proteins that can act with dominant-negative or gain-of-function effects. To avoid the synthesis of these shortened polypeptides, several RNA surveillance systems can be activated to decrease the level of PTC-containing mRNAs. Nonsense-mediated mRNA decay (NMD) ensures an accelerated degradation of mRNAs harboring PTCs by using several key NMD factors such as up-frameshift (UPF) proteins. Another pathway called nonsense-associated altered splicing (NAS) upregulates transcripts that have skipped disturbing PTCs by alternative splicing. Thus, these RNA quality control processes eliminate abnormal PTC-containing mRNAs from the cells by using positive and negative responses. In this review, we describe the general mechanisms of NMD and NAS and their respective involvement in the decay of aberrant immunoglobulin and TCR transcripts in lymphocytes.

Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells

In metazoans, cleavage by the endoribonuclease SMG6 is often the first degradative event in non-sense-mediated mRNA decay (NMD). However, the exact sites of SMG6 cleavage have yet to be determined for any endogenous targets, and most evidence as to the identity of SMG6 substrates is indirect. Here, we use Parallel Analysis of RNA Ends to specifically identify the 5′ termini of decay intermediates whose production is dependent on SMG6 and the universal NMD factor UPF1. In this manner, the SMG6 cleavage sites in hundreds of endogenous NMD targets in human cells have been mapped at high resolution. In addition, a preferred sequence motif spanning most SMG6 cleavage sites has been discovered and validated by mutational analysis. For many SMG6 substrates, depletion of SMG6 resulted in the accumulation of decapped transcripts, an effect indicative of competition between SMG6-dependent and SMG6-independent NMD pathways. These findings provide key insights into the mechanisms by which mRNAs targeted by NMD are degraded.

Quality control of mRNP biogenesis: networking at the transcription site

Eukaryotic cells carry out quality control (QC) over the processes of RNA biogenesis to inactivate or eliminate defective transcripts, and to avoid their production. In the case of protein-coding transcripts, the quality controls can sense defects in the assembly of mRNA-protein complexes, in the processing of the precursor mRNAs, and in the sequence of open reading frames. Different types of defect are monitored by different specialized mechanisms. Some of them involve dedicated factors whose function is to identify faulty molecules and target them for degradation. Others are the result of a more subtle balance in the kinetics of opposing activities in the mRNA biogenesis pathway. One way or another, all such mechanisms hinder the expression of the defective mRNAs through processes as diverse as rapid degradation, nuclear retention and transcriptional silencing. Three major degradation systems are responsible for the destruction of the defective transcripts: the exosome, the 5'-3' exoribonucleases, and the nonsense-mediated mRNA decay (NMD) machinery. This review summarizes recent findings on the cotranscriptional quality control of mRNA biogenesis, and speculates that a protein-protein interaction network integrates multiple mRNA degradation systems with the transcription machinery.

When a ribosome encounters a premature termination codon

In mammalian cells, aberrant transcripts harboring a premature termination codon (PTC) can be generated by abnormal or inefficient biogenesis of mRNAs or by somatic mutation. Truncated polypeptides synthesized from these aberrant transcripts could be toxic to normal cellular functions. However, mammalian cells have evolved sophisticated mechanisms for monitoring the quality of mRNAs. The faulty transcripts harboring PTC are subject to nonsense-mediated mRNA decay (NMD), nonsense-mediated translational repression (NMTR), nonsense-associated alternative splicing (NAS), or nonsense-mediated transcriptional gene silencing (NMTGS). In this review, we briefly outline the molecular characteristics of each pathway and suggest mRNA quality control mechanisms as a means to regulate normal gene expression. [BMB Reports 2013; 46(1): 9-16]

Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells

Promoterless gene trap vectors have been widely used for high-efficiency gene targeting and random mutagenesis in embryonic stem (ES) cells. Unfortunately, such vectors are only effective for genes expressed in ES cells and this has prompted the development of expression-independent vectors. These polyadenylation (poly A) trap vectors employ a splice donor to capture an endogenous gene's polyadenylation sequence and provide transcript stability. However, the spectrum of mutations generated by these vectors appears largely restricted to the last intron of target loci due to nonsense-mediated mRNA decay (NMD) making them unsuitable for gene targeting applications. Here, we present novel poly A trap vectors that overcome the effect of NMD and also employ RNA instability sequences to improve splicing efficiency. The set of random insertions generated with these vectors show a significantly reduced insertional bias and the vectors can be targeted directly to a 5' intron. We also show that this relative positional independence is linked to the human beta-actin promoter and is most likely a result of its transcriptional activity in ES cells. Taken together our data indicate that these vectors are an effective tool for insertional mutagenesis that can be used for either gene trapping or gene targeting.

Processing bodies are not required for mammalian nonsense-mediated mRNA decay

Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality-control mechanism that recognizes and degrades mRNAs with premature termination codons (PTCs). In yeast, PTC-containing mRNAs are targeted to processing bodies (P-bodies), and yeast strains expressing an ATPase defective Upf1p mutant accumulate P-bodies. Here we show that in human cells, an ATPase-deficient UPF1 mutant and a fraction of UPF2 and UPF3b accumulate in cytoplasmic foci that co-localize with P-bodies. Depletion of the P-body component Ge-1, which prevents formation of microscopically detectable P-bodies, also impairs the localization of mutant UPF1, UPF2, and UPF3b in cytoplasmic foci. However, the accumulation of the ATPase-deficient UPF1 mutant in P-bodies is independent of UPF2, UPF3b, or SMG1, and the ATPase-deficient UPF1 mutant can localize into the P-bodies independent of its phosphorylation status. Most importantly, disruption of P-bodies by depletion of Ge-1 affects neither the mRNA levels of PTC-containing reporter genes nor endogenous NMD substrates. Consistent with the recently reported decapping-independent SMG6-mediated endonucleolytic decay of human nonsense mRNAs, our results imply that microscopically detectable P-bodies are not required for mammalian NMD.

SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

From yeast to humans, mRNAs harboring premature termination codons (PTCs) are recognized and degraded by nonsense-mediated mRNA decay (NMD). However, degradation mechanisms of NMD have been suggested to differ between species. In Drosophila melanogaster, NMD is initiated by endonucleolysis near the PTC, whereas in yeast and human cells the current view posits that NMD occurs by exonucleolysis from one or both RNA termini. Here we report that degradation of human nonsense mRNAs can be initiated by PTC-proximal endonucleolytic cleavage. We identify the metazoan-specific NMD factor SMG6 as the responsible endonuclease by demonstrating that mutation of conserved residues in its nuclease domain--the C-terminal PIN motif--abolishes endonucleolysis in vivo and in vitro. Our data lead to a revised mechanistic model for degradation of nonsense mRNA in human cells and suggest that endonucleolytic cleavage is a conserved feature in metazoan NMD.

Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region

Translation termination at premature termination codons (PTCs) triggers degradation of the aberrant mRNA, but the mechanism by which a termination event is defined as premature is still unclear. Here we show that the physical distance between the termination codon and the poly(A)-binding protein PABPC1 is a crucial determinant for PTC recognition in human cells. “Normal” termination codons can trigger nonsense-mediated mRNA decay (NMD) when this distance is extended; and vice versa, NMD can be suppressed by folding the poly(A) tail into proximity of a PTC or by tethering of PABPC1 nearby a PTC, indicating an evolutionarily conserved function of PABPC1 in promoting correct translation termination and antagonizing activation of NMD. Most importantly, our results demonstrate that spatial rearrangements of the 3′ untranslated region can modulate the NMD pathway and thereby provide a novel mechanism for posttranscriptional gene regulation.

Correct expression of the genetic information is essential for life, and several quality control systems have evolved to ensure accurate protein synthesis. One of these processes, termed nonsense-mediated mRNA decay (NMD), detects inappropriate termination of mRNA translation at premature termination codons (PTCs) and triggers degradation of the aberrant mRNA. Although the occurrence of NMD is well documented in yeast, worms, flies, mammals, and plants, the mechanism by which a termination event is defined as premature is still unclear, and different models have been proposed for different species. For mammals, the current prevailing view is that a termination codon is identified as premature and elicits NMD when it is located upstream of the 3′-most exon junction complex. However, well-documented examples of NMD triggered by PTCs in the last exon challenge this “mammalian NMD model.” Here we show that the physical distance between the termination codon and the poly(A)-binding protein PABPC1 is a crucial determinant for PTC recognition in human cells, indicating an evolutionarily conserved function of PABPC1 in promoting correct translation termination and antagonizing activation of NMD. Most importantly, our results demonstrate that spatial rearrangements of the 3′ untranslated region can modulate the NMD pathway and thereby provide a novel, translation-dependent mechanism for posttranscriptional gene regulation.

The physical distance to the poly(A) tail is a crucial determinant to define a termination codon as premature in human cells. This indicates evolutionary conservation of the basic mechanism of nonsense-mediated mRNA decay and provides a novel mechanism for translation-dependent posttranscriptional gene regulation.

Isolated growth hormone deficiency type II caused by a point mutation that alters both splice site strength and splicing enhancer function

A heterozygous single base mutation in the human growth hormone (GH) gene (GH-1) was identified in a family presenting with isolated GH deficiency type II (IGHD II). Affected individuals have a guanine to adenine transition at the first nucleotide of exon 3 (E3+1 G-->A) that results in exon skipping and production of a dominant-negative 17.5-kDa isoform. We show that the mechanistic basis for exon skipping is due to the unique position of this mutation because it weakens the 3' splice site and simultaneously disrupts a splicing enhancer located within the first seven bases of exon 3. A G-->T mutation at this same position not only affects splicing but also results in a premature stop codon for those transcripts that include exon 3. Thus, mutations that alter the first nucleotide of exon 3 illustrate the various mechanisms by which changes in sequence can cause disease: splice site selection, splicing enhancer function, messenger RNA decay, missense mutations, and nonsense mutations. For IGHD II, only exon skipping leads to production of the dominant-negative isoform, with increasing skipping correlating with increasing disease severity.

Translational control of intron splicing in eukaryotes

Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs. In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy.

Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm

The nonsense-mediated mRNA decay (NMD) pathway rids eukaryotic cells of mRNAs with premature termination codons. There is contradictory evidence as to whether mammalian NMD is a nuclear or a cytoplasmic process. Here, we show evidence that NMD in human cells occurs primarily, if not entirely, in the cytoplasm. Polypeptides designed to inhibit interactions between NMD factors specifically impede NMD when exogenously expressed in the cytoplasm. However, restricting the polypeptides to the nucleus strongly impairs their NMD-inhibitory function, even for those intended to inhibit interactions between the exon-junction complex (EJC) and hUpf3 proteins, which localize primarily in the nucleus. NMD substrates classified based on cell fractionation assays as "nucleus associated" or "cytoplasmic" are all inhibited in the same manner. Furthermore, retention of the NMD factor hUpf1 in the nucleus strongly impairs NMD. These observations suggest that the hUpf complex communicates with the EJC and triggers NMD in the cytoplasm.

Alternatively Spliced T-cell Receptor Transcripts Are Up-regulated in Response to Disruption of Either Splicing Elements or Reading Frame

Nonsense mutations create premature termination codons (PTCs), leading to the generation of truncated proteins, some of which have deleterious gain-of-function or dominant-negative activity. Protecting cells from such aberrant proteins is non-sense-mediated decay (NMD), an RNA surveillance pathway that degrades transcripts harboring PTCs. A second response to nonsense mutations is the up-regulation of alternatively spliced transcripts that skip the PTC. This nonsense-associated altered splicing (NAS) response has the potential to rescue protein function, but the mechanism by which it is triggered has been controversial. Some studies suggest that, like NMD, NAS is triggered as a result of nonsense mutations disrupting reading frame, whereas other studies suggest that NAS is triggered when nonsense mutations disrupt exonic splicing enhancers (ESEs). Using T-cell receptor-beta (TCRbeta), which naturally acquires PTCs at high frequency, we provide evidence that both mechanisms act on a single type of mRNA. Mutations that disrupt consensus ESE sites up-regulated an alternatively spliced TCRbeta transcript that skipped the mutations independently of reading frame disruption and the NMD factor UPF1. In contrast, reading frame-disrupting mutations that did not disrupt consensus ESE sites elicited UPF1-dependent up-regulation of the alternatively spliced TCRbeta transcript. Restoration of reading frame prevented this up-regulation. Our results suggest that the response of an mRNA to a nonsense mutation depends on its context.

Association of ribosomal proteins with nascent transcripts in S. cerevisiae

Although it is generally accepted that transcription and translation are spatially separated in eukaryotes, a number of recent observations have called this belief into question. In particular, several studies have shown that parts of the translation machinery, including ribosomal proteins, can be found associated with sites of active transcription in metazoans. Here we describe results of chromatin immunoprecipitation (ChIP) experiments designed to determine whether ribosomal proteins associate with nascent transcripts in Saccharomyces cerevisiae and whether this association reflects a functional engagement of the translation machinery. We find that HAT-tagged ribosomal proteins can be detected in association with nascent RNAs in budding yeast. However, our data clearly indicate that this binding is independent of transcript translatability, so is therefore not indicative of nuclear translation.

Alternative splicing induced by nonsense mutations in the immunoglobulin mu VDJ exon is independent of truncation of the open reading frame

In addition to triggering nonsense-mediated mRNA decay (NMD), premature translation-termination codons (PTCs) frequently induce alternative splicing, an observation referred to as nonsense-associated alternative splicing (NAS). In many cases, NAS is induced because the nonsense mutation alters a splicing signal, such as inactivating an exonic splicing enhancer. However, for a few genes, NAS was reported to be PTC specific, implying that a translation signal could influence splicing. Here, we investigated whether production of a previously undetected alternatively spliced transcript from immunoglobulin mu (Ig-mu) depends on premature termination of the open reading frame. We show that PTCs at different positions in the VDJ exon of an Ig-mu minigene activate usage of an alternative 3' splice site, generating an alternative transcript that lacks the initial PTC and a previously identified NMD-promoting element (NPE), but contains new PTCs because of a frame shift. Corroborating the importance of the NPE for maximal NMD response, the alternative transcript is only moderately down-regulated by NMD. We further demonstrate that NAS of Ig-mu minigene transcripts is not PTC specific. This finding, together with our results that contradict the previously reported frame dependence of TCR-beta NAS, challenges the idea that cells might possess mechanisms that would allow regulation of splice site selection in response to premature termination of the ORF.