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nonsense-mediated degradation

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https://www.readbyqxmd.com/read/28690834/from-disease-modelling-to-personalised-therapy-in-patients-with-cep290-mutations
#1
Elisa Molinari, Shalabh Srivastava, John A Sayer, Simon A Ramsbottom
Mutations that give rise to premature termination codons are a common cause of inherited genetic diseases. When transcripts containing these changes are generated, they are usually rapidly removed by the cell through the process of nonsense-mediated decay. Here we discuss observed changes in transcripts of the centrosomal protein CEP290 resulting not from degradation, but from changes in exon usage. We also comment on a landmark paper (Drivas et al. Sci Transl Med. 2015) where modelling this process of exon usage may be used to predict disease severity in CEP290 ciliopathies, and how understanding this process may potentially be used for therapeutic benefit in the future...
2017: F1000Research
https://www.readbyqxmd.com/read/28669802/the-rna-surveillance-factor-upf1-represses-myogenesis-via-its-e3%C3%A2-ubiquitin-ligase-activity
#2
Qing Feng, Sujatha Jagannathan, Robert K Bradley
UPF1 is an RNA helicase that orchestrates nonsense-mediated decay and other RNA surveillance pathways. While UPF1 is best known for its basal cytoprotective role in degrading aberrant RNAs, UPF1 also degrades specific, normally occurring mRNAs to regulate diverse cellular processes. Here we describe a role for UPF1 in regulated protein decay, wherein UPF1 acts as an E3 ubiquitin ligase to repress human skeletal muscle differentiation. Suppressing UPF1 accelerates myogenesis, while ectopically increasing UPF1 levels slows myogenesis...
June 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28663146/human-nonsense-mediated-rna-decay-regulates-emt-by-targeting-the-tgf-%C3%A3-signaling-pathway-in-lung-adenocarcinoma
#3
Lu Cao, Lisha Qi, Lin Zhang, Wangzhao Song, Yue Yu, Cong Xu, Lingmei Li, Yuhong Guo, Lingyi Yang, Changxu Liu, Qiujuan Huang, Yalei Wang, Baocun Sun, Bin Meng, Bin Zhang, Wenfeng Cao
Nonsense-mediated mRNA decay (NMD) is a highly conserved pathway that selectively degrades aberrant RNA transcripts. In this study, we proved that NMD regulates the epithelial-mesenchymal transition (EMT) of lung adenocarcinoma (ADC). Moreover, we found that NMD core factor UP-frameshift 1 tends to be expressed at lower levels in human ADC tissues than in normal lung tissues, thereby raising the possibility that NMD may be downregulated to permit ADC oncogenesis. Our experiments in human ADC cell lines showed that downregulating NMD can promote EMT...
June 27, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28663100/a-new-aav10-u7-mediated-gene-therapy-prolongs-survival-and-restores-function-in-an-als-mouse-model
#4
Maria Grazia Biferi, Mathilde Cohen-Tannoudji, Ambra Cappelletto, Benoit Giroux, Marianne Roda, Stéphanie Astord, Thibaut Marais, Corinne Bos, Thomas Voit, Arnaud Ferry, Martine Barkats
One of the most promising therapeutic approaches for familial amyotrophic lateral sclerosis linked to superoxide dismutase 1 (SOD1) is the suppression of toxic mutant SOD1 in the affected tissues. Here, we report an innovative molecular strategy for inducing substantial, widespread, and sustained reduction of mutant human SOD1 (hSOD1) levels throughout the body of SOD1(G93A) mice, leading to therapeutic effects in animals. Adeno-associated virus serotype rh10 vectors (AAV10) were used to mediate exon skipping of the hSOD1 pre-mRNA by expression of exon-2-targeted antisense sequences embedded in a modified U7 small-nuclear RNA (AAV10-U7-hSOD)...
June 26, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28615637/defects-in-autophagosome-lysosome-fusion-underlie-vici-syndrome-a-neurodevelopmental-disorder-with-multisystem-involvement
#5
Ikumi Hori, Takanobu Otomo, Mitsuko Nakashima, Fuyuki Miya, Yutaka Negishi, Hideaki Shiraishi, Yutaka Nonoda, Shinichi Magara, Jun Tohyama, Nobuhiko Okamoto, Takeshi Kumagai, Konomi Shimoda, Yoshiya Yukitake, Daigo Kajikawa, Tomohiro Morio, Ayako Hattori, Motoo Nakagawa, Naoki Ando, Ichizo Nishino, Mitsuhiro Kato, Tatsuhiko Tsunoda, Hirotomo Saitsu, Yonehiro Kanemura, Mami Yamasaki, Kenjiro Kosaki, Naomichi Matsumoto, Tamotsu Yoshimori, Shinji Saitoh
Vici syndrome (VICIS) is a rare, autosomal recessive neurodevelopmental disorder with multisystem involvement characterized by agenesis of the corpus callosum, cataracts, cardiomyopathy, combined immunodeficiency, developmental delay, and hypopigmentation. Mutations in EPG5, a gene that encodes a key autophagy regulator, have been shown to cause VICIS, however, the precise pathomechanism underlying VICIS is yet to be clarified. Here, we describe detailed clinical (including brain MRI and muscle biopsy) and genetic features of nine Japanese patients with VICIS...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611678/a-fourth-klk4-mutation-is-associated-with-enamel-hypomineralisation-and-structural-abnormalities
#6
Claire E L Smith, Jennifer Kirkham, Peter F Day, Francesca Soldani, Esther J McDerra, James A Poulter, Christopher F Inglehearn, Alan J Mighell, Steven J Brookes
"Amelogenesis imperfecta" (AI) describes a group of genetic conditions that result in defects in tooth enamel formation. Mutations in many genes are known to cause AI, including the gene encoding the serine protease, kallikrein related peptidase 4 (KLK4), expressed during the maturation stage of amelogenesis. In this study we report the fourth KLK4 mutation to be identified in autosomal recessively-inherited hypomaturation type AI, c.632delT, p.(L211Rfs(*)37) (NM_004917.4, NP_004908.4). This homozygous variant was identified in five Pakistani AI families and is predicted to result in a transcript with a premature stop codon that escapes nonsense mediated decay...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28597146/human-i%C3%AE%C2%BAb%C3%AE-gain-of-function-a-severe-and-syndromic-immunodeficiency
#7
REVIEW
Bertrand Boisson, Anne Puel, Capucine Picard, Jean-Laurent Casanova
Germline heterozygous gain-of-function (GOF) mutations of NFKBIA, encoding IκBα, cause an autosomal dominant (AD) form of anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID). Fourteen unrelated patients have been reported since the identification of the first case in 2003. All mutations enhanced the inhibitory activity of IκBα, by preventing its phosphorylation on serine 32 or 36 and its subsequent degradation. The mutation certainly or probably occurred de novo in 13 patients, whereas it was inherited from a parent with somatic mosaicism in one patient...
July 2017: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/28588666/molecular-analysis-of-the-novel-ids-allele-in-a-thai-family-with-mucopolysaccharidosis-type-ii-the-c-928c-t-p-gln310-transcript-is-sensitive-to-nonsense-mediated-mrna-decay
#8
Lukana Ngiwsara, Kitiwan Rojnueangnit, Duangrurdee Wattanasirichaigoon, Thipwimol Tim-Aroon, Phannee Sawangareetrakul, Voraratt Champattanachai, James R Ketudat-Cairns, Jisnuson Svasti
Hunter syndrome (or mucopolysaccharidosis type II, MPS II) is an X-linked recessive disorder induced by a deficiency of the iduronate 2-sulfatase (IDS) enzyme, resulting in the accumulation of glycosaminoglycan substrates, heparan sulfate and dermatan sulfate, in the lysosomes. The progressive accumulation of undegraded metabolites induces cell and tissue dysfunction, leading to multi-systemic pathology. The heterogeneity of clinical phenotypes, ranging from mild to severe forms, results from different mutations in the IDS gene...
June 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28570605/frameshift-indels-introduced-by-genome-editing-can-lead-to-in-frame-exon-skipping
#9
Simon Lalonde, Oliver A Stone, Samuel Lessard, Adam Lavertu, Jessica Desjardins, Mélissa Beaudoin, Manuel Rivas, Didier Y R Stainier, Guillaume Lettre
The introduction of frameshift indels by genome editing has emerged as a powerful technique to study the functions of uncharacterized genes in cell lines and model organisms. Such mutations should lead to mRNA degradation owing to nonsense-mediated mRNA decay or the production of severely truncated proteins. Here, we show that frameshift indels engineered by genome editing can also lead to skipping of "multiple of three nucleotides" exons. Such splicing events result in in-frame mRNA that may encode fully or partially functional proteins...
2017: PloS One
https://www.readbyqxmd.com/read/28533900/control-of-gene-expression-through-the-nonsense-mediated-rna-decay-pathway
#10
REVIEW
Andrew Nickless, Julie M Bailis, Zhongsheng You
Nonsense-mediated RNA decay (NMD) was originally discovered as a cellular surveillance pathway that safeguards the quality of mRNA transcripts in eukaryotic cells. In its canonical function, NMD prevents translation of mutant mRNAs harboring premature termination codons (PTCs) by targeting them for degradation. However, recent studies have shown that NMD has a much broader role in gene expression by regulating the stability of many normal transcripts. In this review, we discuss the function of NMD in normal physiological processes, its dynamic regulation by developmental and environmental cues, and its association with human disease...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/28508407/structural-conservation-of-the-pin-domain-active-site-across-all-domains-of-life
#11
REVIEW
M Senissar, M C Manav, D E Brodersen
The PIN (PilT N-terminus) domain is a compact RNA-binding protein domain present in all domains of life. This 120-residue domain consists of a central and parallel β sheet surrounded by α helices, which together organize 4-5 acidic residues in an active site that binds one or more divalent metal ions and in many cases has endoribonuclease activity. In bacteria and archaea, the PIN domain is primarily associated with toxin-antitoxin loci, consisting of a toxin (the PIN domain nuclease) and an antitoxin that inhibits the function of the toxin under normal growth conditions...
May 15, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28503708/stress-and-the-nonsense-mediated-rna-decay-pathway
#12
REVIEW
Alexandra E Goetz, Miles Wilkinson
Cells respond to internal and external cellular stressors by activating stress-response pathways that re-establish homeostasis. If homeostasis is not achieved in a timely manner, stress pathways trigger programmed cell death (apoptosis) to preserve organism integrity. A highly conserved stress pathway is the unfolded protein response (UPR), which senses excessive amounts of unfolded proteins in the ER. While a physiologically beneficial pathway, the UPR requires tight regulation to provide a beneficial outcome and avoid deleterious consequences...
May 13, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28461625/transcript-specific-characteristics-determine-the-contribution-of-endo-and-exonucleolytic-decay-pathways-during-the-degradation-of-nonsense-mediated-decay-substrates
#13
Franziska Ottens, Volker Boehm, Christopher R Sibley, Jernej Ule, Niels H Gehring
Nonsense-mediated mRNA decay (NMD) controls gene expression by eliminating mRNAs with premature or aberrant translation termination. Degradation of NMD substrates is initiated by the central NMD factor UPF1, which recruits the endonuclease SMG6 and the deadenylation-promoting SMG5/7 complex. The extent to which SMG5/7 and SMG6 contribute to the degradation of individual substrates and their regulation by UPF1 remain elusive. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3' fragment capture and degradome sequencing...
May 1, 2017: RNA
https://www.readbyqxmd.com/read/28444146/nonsense-in-the-testis-multiple-roles-for-nonsense-mediated-decay-revealed-in-male-reproduction
#14
Clinton C MacDonald, Petar N Grozdanov
Nonsense-mediated mRNA decay, or NMD, is a quality control mechanism that identifies cytoplasmic mRNAs containing translational termination (stop) codons in specific contexts - either premature termination codons or unusually long 3΄ untranslated regions - and targets them for degradation. In recent studies, researchers in different labs have knocked out important genes involved in NMD, Upf2 and Upf3a, and one component of chromatoid bodies, Tdrd6, and examined the consequences for spermatogenesis. Disruption of Upf2 during early stages of spermatogenesis resulted in disappearance of nearly all spermatogenic cells through loss of NMD...
April 22, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28423339/germ-cell-specific-inflammasome-component-nlrp14-negatively-regulates-cytosolic-nucleic-acid-sensing-to-promote-fertilization
#15
Takayuki Abe, Albert Lee, Ramaswami Sitharam, Jordan Kesner, Raul Rabadan, Sagi D Shapira
Cytosolic sensing of nucleic acids initiates tightly regulated programs to limit infection. Oocyte fertilization represents a scenario wherein inappropriate responses to exogenous yet non-pathogen-derived nucleic acids would have negative consequences. We hypothesized that germ cells express negative regulators of nucleic acid sensing (NAS) in steady state and applied an integrated data-mining and functional genomics approach to identify a rheostat of DNA and RNA sensing-the inflammasome component NLRP14. We demonstrated that NLRP14 interacted physically with the nucleic acid sensing pathway and targeted TBK1 (TANK binding kinase 1) for ubiquitination and degradation...
April 18, 2017: Immunity
https://www.readbyqxmd.com/read/28389433/structure-of-a-smg8-smg9-complex-identifies-a-g-domain-heterodimer-in-the-nmd-effector-proteins
#16
Liang Li, Mahesh Lingaraju, Claire Basquin, Jérome Basquin, Elena Conti
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA degradation pathway involved in surveillance and post-transcriptional regulation, and executed by the concerted action of several trans-acting factors. The SMG1 kinase is an essential NMD factor in metazoans and is associated with two recently identified and yet poorly characterized proteins, SMG8 and SMG9. We determined the 2.5 Å resolution crystal structure of a SMG8-SMG9 core complex from C. elegans We found that SMG8-SMG9 is a G-domain heterodimer with architectural similarities to the dynamin-like family of GTPases such as Atlastin and GBP1...
July 2017: RNA
https://www.readbyqxmd.com/read/28383761/endoplasmic-reticulum-stress-in-mice-increases-hepatic-expression-of-genes-carrying-a-premature-termination-codon-via-a-nutritional-status-independent-grp78-dependent-mechanism
#17
Nagakatsu Harada, Maiko Okuyama, Aya Yoshikatsu, Hironori Yamamoto, Saori Ishiwata, Chikako Hamada, Tomoyo Hirose, Masayuki Shono, Masashi Kuroda, Rie Tsutsumi, Jiro Takeo, Yutaka Taketani, Yutaka Nakaya, Hiroshi Sakaue
Nonsense-mediated mRNA decay (NMD) degrades mRNAs carrying a premature termination codon (PTC) in eukaryotes. Cellular stresses, including endoplasmic reticulum (ER) stress, inhibit NMD and up-regulate PTC-containing mRNA (PTC-mRNA) levels in several cell lines. However, whether similar effects exist under in vivo conditions that involve systemic nutritional status is unclear. Here we compared the effects of pharmacological induction of ER stress with those of nutritional interventions on hepatic PTC-mRNA levels in mice...
April 6, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28369084/nmd-classifier-a-reliable-and-systematic-classification-tool-for-nonsense-mediated-decay-events
#18
Min-Kung Hsu, Hsuan-Yu Lin, Feng-Chi Chen
Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/28367323/nonsense-suppression-as-an-approach-to-treat-lysosomal-storage-diseases
#19
Kim M Keeling
In-frame premature termination codons (PTCs) (also referred to as nonsense mutations) comprise ~10% of all disease-associated gene lesions. PTCs reduce gene expression in two ways. First, PTCs prematurely terminate translation of an mRNA, leading to the production of a truncated polypeptide that often lacks normal function and/or is unstable. Second, PTCs trigger degradation of an mRNA by activating nonsense-mediated mRNA decay (NMD), a cellular pathway that recognizes and degrades mRNAs containing a PTC. Thus, translation termination and NMD are putative therapeutic targets for the development of treatments for genetic diseases caused by PTCs...
December 2016: Diseases (Basel)
https://www.readbyqxmd.com/read/28323884/a-system-for-coordinated-analysis-of-translational-readthrough-and-nonsense-mediated-mrna-decay
#20
Stacey L Baker, J Robert Hogg
The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing premature termination codons, limiting the expression of potentially deleterious truncated proteins. This activity positions the pathway as a regulator of the severity of genetic diseases caused by nonsense mutations. Because many genetic diseases result from nonsense alleles, therapeutics inducing readthrough of premature termination codons and/or inhibition of NMD have been of great interest. Several means of enhancing translational readthrough have been reported to concomitantly inhibit NMD efficiency, but tools for systematic analysis of mammalian NMD inhibition by translational readthrough are lacking...
2017: PloS One
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