Facioscapulohumeral muscular dystrophy (FSHD) is a caused by inefficient epigenetic repression of the D4Z4 macrosatellite array and somatic expression DUX4 retrogene. double homeobox transcription factor that normally expressed in testis causes apoptosis FSHD when misexpressed skeletal muscle. The mechanism(s) toxicity muscle incompletely understood. We report DUX4-triggered proteolytic degradation UPF1, central component nonsense-mediated decay (NMD) machinery, associated with profound NMD...

Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of double-homeodomain transcription factor DUX4 in skeletal muscle cells. Many different cell culture models have been developed to study pathophysiology FSHD, frequently based on endogenous expression FSHD cells or control human Although results generated using each model are generally consistent, differences also reported, making it unclear which model(s) faithfully recapitulate and biology. In this study, we...

Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of DUX4 in skeletal muscle cells. a transcription factor that activates genes normally associated with stem cell biology and its FSHD cells results apoptosis. To identify pathways necessary for DUX4-mediated apoptosis, we performed an siRNA screen RD rhabdomyosarcoma line inducible transgene. Our identified components MYC-mediated apoptotic pathway double-stranded RNA (dsRNA) innate immune response as mediators DUX4-induced...

The gene expression pathway from DNA sequence to functional protein is not as straightforward simple depictions of the central dogma might suggest. Each step highly regulated, with complex and only partially understood molecular mechanisms at play. Translation one where “one gene–one protein” paradigm breaks down, often a single mature eukaryotic mRNA leads more than product. One way this occurs through translation reinitiation, in which ribosome starts making initiation site, translates...

Abstract Nonsense-mediated mRNA decay (NMD) is a network of pathways that degrades transcripts undergo premature translation termination. In mammals, NMD can be divided into the exon junction complex (EJC)-enhanced and EJC-independent branches. Fluorescence- luminescence-based reporters have long been effective tools to investigate NMD, yet existing largely focus on EJC-enhanced pathway. Here, we present system for comparative studies NMD. This also enables study NMD-associated outcomes such...

The mRNA transcriptome is currently thought to be partitioned between the cytosol and endoplasmic reticulum (ER) compartments by binary selection; mRNAs encoding cytosolic/nucleoplasmic proteins are translated on free ribosomes, topogenic signal-bearing ER-bound with ER localization being conferred signal-recognition particle pathway. In subgenomic genomic analyses of subcellular partitioning, we report an overlapping distribution signal-encoding mRNAs, both cohorts displaying noncanonical...

The DUX4 transcription factor is encoded by a retrogene embedded in each unit of the D4Z4 macrosatellite repeat. normally expressed cleavage-stage embryo, whereas chromatin repression prevents expression most somatic tissues. Failure this causes facioscapulohumeral muscular dystrophy (FSHD) due to mis-expression skeletal muscle. In study, we used CRISPR/Cas9 engineered immunoprecipitation (enChIP) locus-specific proteomics characterize D4Z4-associated proteins. These and other approaches...

Signal sequence-encoding mRNAs undergo translation-dependent localization to the endoplasmic reticulum (ER) and at ER are anchored via translation on Sec61-bound ribosomes. Recent investigations into composition membrane association characteristics of ER-associated have, however, revealed both ribosome-dependent (indirect) ribosome-independent (direct) modes mRNA with ER. These findings raise important questions regarding our understanding how selected, localized, Using semi-intact tissue...

Stress granules (SGs) are membraneless organelles composed of mRNAs and RNA binding proteins which undergo assembly in response to stress-induced inactivation translation initiation. In general, SG recruitment is limited a subpopulation given mRNA species RNA-seq analyses purified SGs revealed that signal sequence-encoding (i.e., endoplasmic reticulum [ER]-targeted) transcripts significantly underrepresented, consistent with prior reports ER localization can protect from recruitment. Using...

The specialized protein synthesis functions of the cytosol and endoplasmic reticulum compartments are conferred by signal recognition particle (SRP) pathway, which directs cotranslational trafficking sequence-encoding mRNAs from to (ER). Although subcellular mRNA distributions largely mirror binary pattern predicted SRP pathway model, studies in mammalian cells, yeast, Drosophila have also demonstrated that cytosolic protein-encoding broadly represented on ER-bound ribosomes. A mechanism for...

DUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). DUX4’s transcriptional activity has been extensively characterized, but the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels DUX4-expressing cells via RNA-seq quantitative mass spectrometry. targets were robustly translated, confirming likely clinical relevance proposed FSHD biomarkers. However, multitude mRNAs...

Nonsense-mediated RNA decay (NMD) degrades transcripts carrying premature termination codons. NMD is thought to prevent the synthesis of toxic truncated proteins. However, whether loss results in widespread production proteins unclear. A human genetic disease, facioscapulohumeral muscular dystrophy (FSHD), features acute inhibition upon expression disease-causing transcription factor, DUX4. Using a cell-based model FSHD, we show from physiological targets and find that RNA-binding are...

Genetic variants that disrupt protein-coding DNA are ubiquitous in the human population, with about 100 such loss-of-function per individual. While most rare, a subset have risen to high frequency and occur homozygous state healthy individuals. It is unknown why these common well tolerated, even though some affect essential genes implicated Mendelian disease. Here, we combine genomic, proteomic, biochemical data demonstrate many nonsense do not ablate protein production from their host...

With the aim of evaluating usefulness an in vitro system for assessing potential hepatotoxicity compounds, paper describes several methods obtaining mathematical models prediction compound-induced toxicity vivo. These are based on data derived from treating rat primary hepatocytes with various and thereafter using microarrays to obtain gene expression 'profiles' each compound. Predictive were constructed so as reduce number 'probesets' (genes) required, subjected rigorous cross-validation....

Nearly thirty percent of all newly synthesized polypeptides are targeted for rapid proteasome-mediated degradation. These rapidly degraded (RDPs) a source antigenic substrates the MHC class I presentation pathway, allowing immunosurveillance proteins by cytotoxic T lymphocytes. Despite recognized role RDPs in presentation, it remains unclear what molecular characteristics distinguish from their more stable counterparts. It has been proposed that premature translational termination products...

ABSTRACT Nonsense variants underlie many genetic diseases. The phenotypic impact of nonsense is determined by nonsense-mediated mRNA decay (NMD), which degrades transcripts with premature termination codons (PTCs). Despite its clinical importance, the factors controlling transcript-specific and context-dependent variation in NMD activity remain poorly understood. Through analysis human datasets, we discovered that amino acid preceding PTC strongly influences activity. Notably, glycine...

Translational control is critical for cell fate transitions during development, lineage specification, and tumorigenesis. Here, we show that the transcription factor double homeobox protein 4 (DUX4), its previously characterized transcriptional program, broadly regulates translation to change cellular proteome. DUX4 a key regulator of zygotic genome activation in human embryos, whereas misexpression causes facioscapulohumeral muscular dystrophy (FSHD) associated with MHC-I suppression immune...