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nonsense-mediated decay

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https://www.readbyqxmd.com/read/28917839/m2b-macrophage-polarization-accompanied-with-reduction-of-long-noncoding-rna-gas5
#1
Ichiaki Ito, Akira Asai, Sumihiro Suzuki, Makiko Kobayashi, Fujio Suzuki
Macrophages (Mϕ) are highly plastic and change their functional phenotypes depending on microenvironmental signals. Recent studies have shown that microRNAs are involved in the polarization of Mϕ. In this study, we demonstrated that the phenotype of M2bMϕ [CCL1(+) IL-10(+) LIGHT(+)] switches to other phenotypes with interchangeability attained through the increased expression of growth arrest-specific 5 RNA (GAS5 RNA), a long non-coding RNA. GAS5 RNA has been described as a silencer of the CCL1 gene. Various phenotypes of Mϕ were prepared from bone marrow-derived Mϕ (BMDMϕ) after stimulation with IFNγ [M(IFNγ)]/M1Mϕ, IL-4 [M(IL-4)]/M2aMϕ, LPS and immobilized IgG [M(LPS + IC)]/M2bMϕ, and IL-10 [M(IL-10)/M2cMϕ]...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28905073/erratum-to-stress-and-the-nonsense-mediated-rna-decay-pathway
#2
Alexandra E Goetz, Miles Wilkinson
The original version of this article unfortunately contained errors in the section entitled "NMD in stress responses in plants".
September 13, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28899899/dual-function-of-upf3b-in-early-and-late-translation-termination
#3
Gabriele Neu-Yilik, Etienne Raimondeau, Boris Eliseev, Lahari Yeramala, Beate Amthor, Aurélien Deniaud, Karine Huard, Kathrin Kerschgens, Matthias W Hentze, Christiane Schaffitzel, Andreas E Kulozik
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance pathway that recognizes and degrades mRNAs with premature termination codons (PTCs). The mechanisms underlying translation termination are key to the understanding of RNA surveillance mechanisms such as NMD and crucial for the development of therapeutic strategies for NMD-related diseases. Here, we have used a fully reconstituted in vitro translation system to probe the NMD proteins for interaction with the termination apparatus. We discovered that UPF3B (i) interacts with the release factors, (ii) delays translation termination and (iii) dissociates post-termination ribosomal complexes that are devoid of the nascent peptide...
September 12, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28894297/the-pnkd-gene-is-associated-with-tourette-disorder-or-tic-disorder-in-a-multiplex-family
#4
N Sun, C Nasello, L Deng, N Wang, Y Zhang, Z Xu, Z Song, K Kwan, R A King, Z P Pang, J Xing, G A Heiman, J A Tischfield
Tourette Disorder (TD) is a childhood-onset neuropsychiatric and neurodevelopmental disorder characterized by the presence of both motor and vocal tics. The genetic architecture of TD is believed to be complex and heterogeneous. Nevertheless, DNA sequence variants co-segregating with TD phenotypes within multiplex families have been identified. This report examines whole exomes of affected and unaffected individuals in a multiplex TD family to discover genes involved in the TD etiology. We performed whole exome sequencing on six out of nine members in a three-generation TD multiplex family...
September 12, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28890334/crispr-mediated-base-editing-enables-efficient-disruption-of-eukaryotic-genes-through-induction-of-stop-codons
#5
Pierre Billon, Eric E Bryant, Sarah A Joseph, Tarun S Nambiar, Samuel B Hayward, Rodney Rothstein, Alberto Ciccia
Standard CRISPR-mediated gene disruption strategies rely on Cas9-induced DNA double-strand breaks (DSBs). Here, we show that CRISPR-dependent base editing efficiently inactivates genes by precisely converting four codons (CAA, CAG, CGA, and TGG) into STOP codons without DSB formation. To facilitate gene inactivation by induction of STOP codons (iSTOP), we provide access to a database of over 3.4 million single guide RNAs (sgRNAs) for iSTOP (sgSTOPs) targeting 97%-99% of genes in eight eukaryotic species, and we describe a restriction fragment length polymorphism (RFLP) assay that allows the rapid detection of iSTOP-mediated editing in cell populations and clones...
September 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28878343/plasmid-transfection-influences-the-readout-of-nonsense-mediated-mrna-decay-reporter-assays-in-human-cells
#6
Jennifer V Gerbracht, Volker Boehm, Niels H Gehring
Messenger RNA (mRNA) turnover is a crucial and highly regulated step of gene expression in mammalian cells. This includes mRNA surveillance pathways such as nonsense-mediated mRNA decay (NMD), which assesses the fidelity of transcripts and eliminates mRNAs containing a premature translation termination codon (PTC). When studying mRNA degradation pathways, reporter mRNAs are commonly expressed in cultivated cells. Traditionally, the molecular mechanism of NMD has been characterized using pairs of reporter constructs that express the same mRNA with ("PTC-containing mRNA") or without ("wild-type mRNA") a PTC...
September 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28874147/assessing-the-activity-of-nonsense-mediated-mrna-decay-in-lung-cancer
#7
Meng Wang, Peiwei Zhang, Yufei Zhu, Xiangyin Kong, Zhenguo Zhang, Landian Hu
BACKGROUND: Inhibition of nonsense-mediated mRNA decay (NMD) in tumor cells can suppress tumor growth through expressing new antigens whose mRNAs otherwise are degraded by NMD. Thus NMD inhibition is a promising approach for developing cancer therapies. Apparently, the success of this approach relies on the basal NMD activity in cancer cells. If NMD is already strongly inhibited in tumors, the approach would not work. Therefore, it is crucial to assess NMD activity in cancers to forecast the efficacy of NMD-inhibition based therapy...
September 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28870597/spastic-paraplegia-type-4-a-novel-spast-splice-site-donor-mutation-and-expansion-of-the-phenotype-variability
#8
Toshitaka Kawarai, Celeste Montecchiani, Ryosuke Miyamoto, Fabrizio Gaudiello, Carlo Caltagirone, Yuishin Izumi, Ryuji Kaji, Antonio Orlacchio
Mutations in SPG4/SPAST are the most frequent molecular aetiology in the autosomal dominant form of hereditary spastic paraplegia (HSP). Loss-of-function and haploinsufficiency in SPAST have been demonstrated and the pure form of spastic paraplegia is a main clinical manifestation. This study is to explore the novel SPAST splice site donor variant, c.1004+3A>C, in seven patients from two families, one from Italy and the other from Japan. Exon 6 is skipped out by the variant, leading to a premature termination of translation, p...
September 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28866327/beyond-quality-control-the-role-of-nonsense-mediated-mrna-decay-nmd-in-regulating-gene-expression
#9
REVIEW
Sofia Nasif, Lara Contu, Oliver Mühlemann
Nonsense-mediated mRNA decay (NMD) has traditionally been described as a quality control system that rids cells of aberrant mRNAs with crippled protein coding potential. However, transcriptome-wide profiling of NMD deficient cells identified a plethora of seemingly intact mRNAs coding for functional proteins as NMD targets. This led to the view that NMD constitutes an additional post-transcriptional layer of gene expression control involved in the regulation of many different biological pathways. Here, we review our current knowledge about the role of NMD in embryonic development and tissue-specific cell differentiation...
September 1, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28841713/processing-of-opa1-with-a-novel-n-terminal-mutation-in-patients-with-autosomal-dominant-optic-atrophy-escape-from-nonsense-mediated-decay
#10
Aneta Ścieżyńska, Ewelina Ruszkowska, Kamil Szulborski, Katarzyna Rydz, Joanna Wierzbowska, Joanna Kosińska, Marek Rękas, Rafał Płoski, Jacek Paweł Szaflik, Monika Ołdak
Autosomal Dominant Optic Atrophy (ADOA) is the most common dominantly inherited optic neuropathy. In the majority of patients it is caused by OPA1 mutations and those predicted to introduce a premature termination codon (PTC) are frequently detected. Transcripts containing PTC may be degraded by nonsense-mediated mRNA decay (NMD), however very little is known about an effect of OPA1 mutations on NMD activation. Here, using a combination of linkage analysis and DNA sequencing, we have identified a novel c.91C>T OPA1 mutation with a putative premature stop codon (Q31*), which segregated with ADOA in two Polish families...
2017: PloS One
https://www.readbyqxmd.com/read/28834196/advanced-cell-based-modeling-of-the-royal-disease-characterization-of-the-mutated-f9-mrna
#11
L Martorell, E Luce, J L Vazquez, Y Richaud-Patin, S Jimenez-Delgado, I Corrales, N Borras, S Casacuberta-Serra, A Weber, R Parra, C Altisent, A Follenzi, A Dubart-Kupperschmitt, A Raya, F Vidal, J Barquinero
BACKGROUND: The royal disease (RD) is a form of hemophilia B that affected many descendants of Queen Victoria in the 19(th) and 20(th) centuries. It was found to be due to the mutation F9 c.278-3A>G. OBJECTIVE: To generate a physiological cell model of the disease and to study F9 expression at the RNA level. METHODS: Using fibroblasts from skin biopsies of a previously identified hemophilic patient bearing the F9 c.278-3A>G mutation and his mother, we generated induced pluripotent stem cells (iPSCs)...
August 21, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28825595/histone-methyltransferase-setd2-modulates-alternative-splicing-to-inhibit-intestinal-tumorigenesis
#12
Huairui Yuan, Ni Li, Da Fu, Jiale Ren, Jingyi Hui, Junjie Peng, Yongfeng Liu, Tong Qiu, Min Jiang, Qiang Pan, Ying Han, Xiaoming Wang, Qintong Li, Jun Qin
The histone H3K36 methyltransferase SETD2 is frequently mutated or deleted in a variety of human tumors. Nevertheless, the role of SETD2 loss in oncogenesis remains largely undefined. Here, we found that SETD2 counteracts Wnt signaling and its inactivation promotes intestinal tumorigenesis in mouse models of colorectal cancer (CRC). SETD2 was not required for intestinal homeostasis under steady state; however, upon irradiation, genetic inactivation of Setd2 in mouse intestinal epithelium facilitated the self-renewal of intestinal stem/progenitor cells as well as tissue regeneration...
September 1, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28821679/upf1-governs-synaptic-plasticity-through-association-with-a-stau2-rna-granule
#13
Tyson E Graber, Erika Freemantle, Mina Anadolu, Sarah Hébert-Seropian, Robyn MacAdam, Unkyung Shin, Huy-Dung Hoang, Tommy Alain, Jean-Claude Lacaille, Wayne S Sossin
Neuronal mRNAs can be packaged in reversibly stalled polysome granules prior to their transport to distant synaptic locales. Stimulation of synaptic metabotropic glutamate receptors (mGluRs) reactivates translation of these particular mRNAs to produce plasticity-related protein; a phenomenon exhibited during mGluR-mediated long-term depression (mGluR-LTD). This form of plasticity is deregulated in Fragile X Syndrome, a monogenic form of autism in humans, and understanding the stalling and reactivation mechanism could reveal new approaches to therapies...
August 18, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28813618/whole-exome-sequencing-identifies-novel-variants-for-tooth-agenesis
#14
N Dinckan, R Du, L E Petty, Z Coban-Akdemir, S N Jhangiani, I Paine, E H Baugh, A P Erdem, H Kayserili, H Doddapaneni, J Hu, D M Muzny, E Boerwinkle, R A Gibbs, J R Lupski, Z O Uyguner, J E Below, A Letra
Tooth agenesis is a common craniofacial abnormality in humans and represents failure to develop 1 or more permanent teeth. Tooth agenesis is complex, and variations in about a dozen genes have been reported as contributing to the etiology. Here, we combined whole-exome sequencing, array-based genotyping, and linkage analysis to identify putative pathogenic variants in candidate disease genes for tooth agenesis in 10 multiplex Turkish families. Novel homozygous and heterozygous variants in LRP6, DKK1, LAMA3, and COL17A1 genes, as well as known variants in WNT10A, were identified as likely pathogenic in isolated tooth agenesis...
August 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28801591/new-variant-and-expression-studies-provide-further-insight-into-the-genotype-phenotype-correlation-in-yap1-related-developmental-eye-disorders
#15
R Holt, F Ceroni, D A Bax, S Broadgate, D Gold Diaz, C Santos, D Gerrelli, N K Ragge
YAP1, which encodes the Yes-associated protein 1, is part of the Hippo pathway involved in development, growth, repair and homeostasis. Nonsense YAP1 mutations have been shown to co-segregate with autosomal dominantly inherited coloboma. Therefore, we screened YAP1 for variants in a cohort of 258 undiagnosed UK patients with developmental eye disorders, including anophthalmia, microphthalmia and coloboma. We identified a novel 1 bp deletion in YAP1 in a boy with bilateral microphthalmia and bilateral chorioretinal coloboma...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28766288/in-vitro-modulation-of-endogenous-alternative-splicing-using-splice-switching-antisense-oligonucleotides
#16
Jeong Eun Park, Luca Cartegni
Regulation of alternative splicing can be harnessed by antisense-based compounds to control gene expression. Antisense-mediated splicing interference has become a valuable molecular tool to modulate endogenous alternative splicing patterns, to correct cryptic or aberrant splicing, to reduce gene expression by triggering nonsense-mediated mRNA decay, and to activate intronic polyadenylation, both in vitro and in vivo. Here, we describe methods to induce and analyze the modulation of RNA processing, using modified splice-switching antisense oligonucleotides, such as phosphorodiamidate morpholino (PMO)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28765281/p38-mapk-inhibits-nonsense-mediated-rna-decay-in-response-to-persistent-dna-damage-in-non-cycling-cells
#17
Andrew Nickless, Abigael Cheruiyot, Kevin C Flanagan, David Piwnica-Worms, Sheila A Stewart, Zhongsheng You
Persistent DNA damage induces profound alterations in gene expression, which in turn influence tissue homeostasis, tumorigenesis, and cancer treatment outcome. However, the underlying mechanism for the gene expression reprogramming induced by persistent DNA damage remains poorly understood. Here, using a highly effective bioluminescence-based reporter system and other tools, we report that persistent DNA damage inhibits nonsense-mediated RNA decay (NMD), an RNA surveillance and gene-regulatory pathway, in noncycling cells...
August 1, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28763028/rous-sarcoma-virus-rna-stability-element-inhibits-deadenylation-of-mrnas-with-long-3-utrs
#18
Vidya Balagopal, Karen L Beemon
All retroviruses use their full-length primary transcript as the major mRNA for Group-specific antigen (Gag) capsid proteins. This results in a long 3' untranslated region (UTR) downstream of the termination codon. In the case of Rous sarcoma virus (RSV), there is a 7 kb 3'UTR downstream of the gag terminator, containing the pol, env, and src genes. mRNAs containing long 3'UTRs, like those with premature termination codons, are frequently recognized by the cellular nonsense-mediated mRNA decay (NMD) machinery and targeted for degradation...
August 1, 2017: Viruses
https://www.readbyqxmd.com/read/28754723/a-functional-link-between-bir1-and-the-saccharomyces-cerevisiae-ctf19-kinetochore-complex-revealed-through-quantitative-fitness-analysis
#19
Vasso Makrantoni, Adam Ciesiolka, Conor Lawless, Josefin Fernius, Adele Marston, David Lydall, Michael J R Stark
The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional proteins (Survivin/Bir1 and Borealin/Nbl1). Here, we report a genome-wide genetic interaction screen in Saccharomyces cerevisiae using the bir1-17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers and suppressors. Gene knockouts affecting the Ctf19 kinetochore complex were identified as the strongest enhancers of bir1-17, while mutations affecting the large ribosomal subunit or the mRNA nonsense-mediated decay pathway caused strong phenotypic suppression...
September 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28743738/ptc-readthrough-in-human-cells-occurs-in-novel-cytoplasmic-foci-and-requires-upf-proteins
#20
Jieshuang Jia, Elisabeth Werkmeister, Sara Gonzalez-Hilarion, Catherine Leroy, Dieter C Gruenert, Frank Lafont, David Tulasne, Fabrice Lejeune
Nonsense-mutation-containing messenger ribonucleoprotein particles (mRNPs) transit through cytoplasmic foci called P-bodies before undergoing nonsense-mediated mRNA decay (NMD), a cytoplasmic mRNA surveillance mechanism. This study shows that the cytoskeleton modulates transport of nonsense-mutation-containing mRNPs to and from P-bodies. Impairing the integrity of cytoskeleton causes inhibition of NMD. The cytoskeleton thus plays a crucial role in NMD. Interestingly, disruption of actin filaments results in both inhibition of NMD and activation of readthrough, while disruption of microtubules causes only NMD inhibition...
July 25, 2017: Journal of Cell Science
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