Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses — adaptation, differentiation or death — to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. In this Review, we discuss how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal mRNAs to control the quantities of unmutated transcripts. Nonsense-mediated mRNA decay (NMD) is a quality and quantity control mechanism for degrading mutated mRNAs to protect the integrity of the transcriptome and proteome and unmutated mRNAs to control their quantity. NMD dysfunction in humans is associated with intellectual disability and cancer.

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Quality and quantity control of gene expression by nonsense-mediated mRNA decay

Background Burnout among physicians affects mental health, performance, and patient outcomes. Surgery residency is a high-risk time for burnout. We examined burnout and the psychological characteristics that can contribute to burnout vulnerability and resilience in a group of surgical trainees. Study Design An online survey was distributed in September 2016 to all ACGME-accredited general surgery programs. Burnout was assessed with an abbreviated Maslach Burnout Inventory. Stress, anxiety, depression, resilience, mindfulness, and alcohol use were assessed and analyzed for prevalence. Odds ratios (ORs) were used to determine the magnitude of presumed risk and resilience factors. Results Among 566 surgical residents who participated in the survey, prevalence of burnout was 69%, equally driven by emotional exhaustion and depersonalization. Perceived stress and distress symptoms (depression, suicidal ideation, and anxiety) were notably high across training levels, but improved during lab years. Higher burnout was associated with high stress (OR 7.8; p  Conclusions High levels of burnout, severe stress, and distress symptoms are experienced throughout general surgery training, with some improvement during lab years. In this cross-sectional study, trainees with burnout and high stress were at increased risk for depression and suicidal ideation. Higher dispositional mindfulness was associated with lower risk of burnout, severe stress, and distress symptoms, supporting the potential of mindfulness training to promote resilience during surgery residency.

Burnout and Stress Among US Surgery Residents: Psychological Distress and Resilience.

The burnout syndrome is characterized by emotional exhaustion, depersonalization, and reduced personal achievement. Uncertainty exists about the prevalence of burnout among medical and surgical residents. Associations between burnout and gender, age, specialty, and geographical location of training are unclear. In this meta-analysis, we aimed to quantitatively summarize the global prevalence rates of burnout among residents, by specialty and its contributing factors. We searched PubMed, PsycINFO, Embase, and Web of Science to identify studies that examined the prevalence of burnout among residents from various specialties and countries. The primary outcome assessed was the aggregate prevalence of burnout among all residents. The random effects model was used to calculate the aggregate prevalence, and heterogeneity was assessed by I2 statistic and Cochran’s Q statistic. We also performed meta-regression and subgroup analysis. The aggregate prevalence of burnout was 51.0% (95% CI: 45.0–57.0%, I2 = 97%) in 22,778 residents. Meta-regression found that the mean age (β = 0.34, 95% CI: 0.28–0.40, p < 0.001) and the proportion of males (β = 0.4, 95% CI = 0.10–0.69, p = 0.009) were significant moderators. Subgroup analysis by specialty showed that radiology (77.16%, 95% CI: 5.99–99.45), neurology (71.93%, 95% CI: 65.78–77.39), and general surgery (58.39%, 95% CI: 45.72–70.04) were the top three specialties with the highest prevalence of burnout. In contrast, psychiatry (42.05%, 95% CI: 33.09–51.58), oncology (38.36%, 95% CI: 32.69–44.37), and family medicine (35.97%, 95% CI: 13.89–66.18) had the lowest prevalence of burnout. Subgroup analysis also found that the prevalence of burnout in several Asian countries was 57.18% (95% CI: 45.8–67.85); in several European countries it was 27.72% (95% CI: 17.4–41.11) and in North America it was 51.64% (46.96–56.28). Our findings suggest a high prevalence of burnout among medical and surgical residents. Older and male residents suffered more than their respective counterparts.

https://www.mdpi.com/1660-4601/16/9/1479/pdf

Prevalence of Burnout in Medical and Surgical Residents: A Meta-Analysis.

Traditional annotation of protein-encoding genes relied on assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it is becoming clear that these initial assumptions are incorrect. The findings have led to the realization that genetic information is more densely coded and that the proteome is more complex than previously anticipated. As such, interest in the identification and characterization of the previously ignored 'dark proteome' is increasing, though we note that research in eukaryotes and bacteria has largely progressed in isolation. To bridge this gap and illustrate exciting findings emerging from studies of the dark proteome, we highlight recent advances in both eukaryotic and bacterial cells. We discuss progress in the detection of alternative ORFs as well as in the understanding of functions and the regulation of their expression and posit questions for future work.

Alternative ORFs and small ORFs: shedding light on the dark proteome.

Nonsense-mediated mRNA decay (NMD) is arguably the best-studied eukaryotic messenger RNA (mRNA) surveillance pathway, yet fundamental questions concerning the molecular mechanism of target RNA selection remain unsolved. Besides degrading defective mRNAs harboring premature termination codons (PTCs), NMD also targets many mRNAs encoding functional full-length proteins. Thus, NMD impacts on a cell's transcriptome and is implicated in a range of biological processes that affect a broad spectrum of cellular homeostasis. Here, we focus on the steps involved in the recognition of NMD targets and the activation of NMD. We summarize the accumulating evidence that tightly links NMD to translation termination and we further discuss the recruitment and activation of the mRNA degradation machinery and the regulation of this complex series of events. Finally, we review emerging ideas concerning the mechanistic details of NMD activation and the potential role of NMD as a general surveyor of translation efficacy.

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Nonsense-Mediated mRNA Decay Begins Where Translation Ends

Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression, yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we reevaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several noncoding RNAs. The vast majority of NMD-regulated transcripts are normal-looking protein-coding mRNAs. Our bioinformatics analyses reveal that this set of NMD-regulated transcripts generally have lower translational efficiency and higher ratios of out-of-frame translation. NMD-regulated transcripts also have lower average codon optimality scores and higher transition probability to nonoptimal codons. Collectively, our results generate a comprehensive catalog of yeast NMD substrates and yield new insights into the mechanisms by which these transcripts are targeted by NMD.

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High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection

We investigated hypothesized risk and resilience factors and their association with burnout in first year medicine and psychiatry residents at an urban teaching hospital in order to help guide the development of interventions targeted at reducing burnout. We administered the Maslach Burnout Inventory (MBI), Perceived Stress Scale-10, Functional Assessment of Chronic Illness Therapy–Fatigue Scale, Penn State Worry Questionnaire, Patient Health Questionnaire-9 (depression symptoms), Revised Life Orientation Test (optimism), Self-Efficacy Questionnaire, Cognitive and Affective Mindfulness Scale, Interpersonal Reactivity Index Perspective-Taking Scale (empathy), and Measure of Current Status-Part A to first year medicine and psychiatry residents prior to initiation of clinical rotations in June. The response rate was 91 % (68 of 75 residents). Nineteen respondents (28 %) met criteria for burnout as measured by the MBI. Residents with burnout scored higher on self-report measures assessing perceived stress (Cohen’s d = 0.97; p = 0.004), fatigue (d = 0.79; p = 0.018), worry (d = 0.88; p = 0.0009), and depression symptoms (d = 0.84; p = 0.035) and scored lower on questionnaires assessing mindfulness (d = −0.63; p = 0.029) and coping ability (d = −0.79; p = 0.003). In a cross-sectional assessment using self-report measures, we found that nearly a third of first year residents prior to starting their internships experience burnout. They exhibit lower levels of mindfulness and coping skills and higher levels of depression symptoms, fatigue, worry, and stress. These preliminary findings should encourage programs to initiate and study curricula that combine mindfulness and self-awareness coping strategies to enhance or protect against burnout as well as cognitive behavioral coaching strategies to offset symptoms of burnout when present.

Risk and Resilience Factors Associated with Resident Burnout.

NMD: At the crossroads between translation termination and ribosome recycling.

The Dcp1-Dcp2 decapping enzyme and the decapping activators Pat1, Dhh1, and Lsm1 regulate mRNA decapping, but their mechanistic integration is unknown. We analyzed the gene expression consequences of deleting PAT1, LSM1, or DHH1, or the DCP2 C-terminal domain, and found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap, are generally translated inefficiently, and, as expected, are targeted to decapping-dependent decay. Our results define the roles of Pat1, Lsm1, and Dhh1 in decapping of general mRNAs and suggest that these factors may monitor mRNA translation and target unique features of individual mRNAs.

General decapping activators target different subsets of inefficiently translated mRNAs.

Nonsense-mediated mRNA decay (NMD) is generally thought to be a eukaryotic mRNA surveillance pathway tasked with the elimination of transcripts harboring an in-frame premature termination codon (PTC) As presently conceived, NMD acting in this manner minimizes the likelihood that potentially toxic polypeptide fragments would accumulate in the cytoplasm This notion is to be contrasted to the results of systematic RNA-Seq and microarray analyses of NMD substrates in multiple model systems, two different experimental approaches which have shown that many mRNAs identified as NMD substrates fail to contain a PTC Our recent results provide insight into, as well as a possible solution for, this conundrum By high-resolution profiling of mRNAs that accumulate in yeast when the principal NMD regulatory genes (UPF1, UPF2, and UPF3) are deleted, we identified approximately 900 NMD substrates, the majority of which are normal-looking mRNAs that lack PTCs Analyses of ribosomal profiling data revealed that the latter mRNAs tended to manifest elevated rates of out-of-frame translation, a phenomenon that would lead to premature translation termination in alternative reading frames These results, and related observations of heterogeneity in mRNA isoforms, suggest that NMD should be reconsidered as a probabilistic mRNA quality control pathway that is continually active throughout an mRNA's life cycle

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Alper Celik

Papers

High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection

Risk and Resilience Factors Associated with Resident Burnout.

NMD: At the crossroads between translation termination and ribosome recycling.

General decapping activators target different subsets of inefficiently translated mRNAs.

NMD monitors translational fidelity 24/7.