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https://www.readbyqxmd.com/read/30147646/clinical-phenotypes-associated-to-engrailed-2-gene-alterations-in-a-series-of-neuropediatric-patients
#1
Francisco Carratala-Marco, Patricia Andreo-Lillo, Marta Martinez-Morga, Teresa Escamez-Martínez, Arancha Botella-López, Carlos Bueno, Salvador Martinez
The engrailed homeobox protein (EN) plays an important role in the regionalization of the neural tube. EN distribution regulates the cerebellum and midbrain morphogenesis, as well as retinotectal synaptogenesis. In humans, the EN1 and EN2 genes code for the EN family of transcription factors. Genetic alterations in the expression of EN2 have been related to different neurologic conditions and more particularly to autism spectrum disorders (ASD). We aimed to study and compare the phenotypes of three series of patients: (1) patients with encephalic structural anomalies (ESA) and abnormalities in the genomic (DNA) and/or transcriptomic (RNAm) of EN2 (EN2-g), (2) ESA patients having other gene mutations (OG-g), and (3) ESA patients free of these mutations (NM-g)...
2018: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/30065031/the-no-go-and-nonsense-mediated-rna-decay-pathways-are-regulated-by-inflammatory-cytokines-in-insulin-producing-cells-and-human-islets-and-determine-%C3%AE-cell-insulin-biosynthesis-and-survival
#2
Seyed Mojtaba Ghiasi, Nicolai Krogh, Björn Tyrberg, Thomas Mandrup-Poulsen
Stress-related changes in β-cell mRNA levels result from a balance between gene transcription and mRNA decay. The regulation of RNA decay pathways has not been investigated in pancreatic β-cells. We found that no-go and nonsense-mediated RNA decay pathway components (RDPCs) and exoribonuclease complexes were expressed in INS-1 cells and human islets. Pelo, Dcp2, Dis3L2, Upf2, and Smg1/5/6/7 were upregulated by inflammatory cytokines in INS-1 cells under conditions where central β-cell mRNAs were downregulated...
October 2018: Diabetes
https://www.readbyqxmd.com/read/29954456/the-rna-surveillance-proteins-upf1-upf2-and-smg6-affect-hiv-1-reactivation-at-a-post-transcriptional-level
#3
Shringar Rao, Raquel Amorim, Meijuan Niu, Abdelkrim Temzi, Andrew J Mouland
BACKGROUND: The ability of human immunodeficiency virus type 1 (HIV-1) to form a stable viral reservoir is the major obstacle to an HIV-1 cure and post-transcriptional events contribute to the maintenance of viral latency. RNA surveillance proteins such as UPF1, UPF2 and SMG6 affect RNA stability and metabolism. In our previous work, we demonstrated that UPF1 stabilises HIV-1 genomic RNA (vRNA) and enhances its translatability in the cytoplasm. Thus, in this work we evaluated the influence of RNA surveillance proteins on vRNA expression and, as a consequence, viral reactivation in cells of the lymphoid lineage...
June 28, 2018: Retrovirology
https://www.readbyqxmd.com/read/29903866/multiple-nonsense-mediated-mrna-processes-require-smg5-in-drosophila
#4
Jonathan O Nelson, Dominique Förster, Kimberly A Frizzell, Stefan Luschnig, Mark M Metzstein
The nonsense-mediated messenger RNA (mRNA) decay (NMD) pathway is a cellular quality control and post-transcriptional gene regulatory mechanism and is essential for viability in most multicellular organisms . A complex of proteins has been identified to be required for NMD function to occur; however, there is an incomplete understanding of the individual contributions of each of these factors to the NMD process. Central to the NMD process are three proteins, Upf1 (SMG-2), Upf2 (SMG-3), and Upf3 (SMG-4), which are found in all eukaryotes, with Upf1 and Upf2 being absolutely required for NMD in all organisms in which their functions have been examined...
August 2018: Genetics
https://www.readbyqxmd.com/read/29667179/characteristics-of-genomic-alterations-of-lung-adenocarcinoma-in-young-never-smokers
#5
Wenxin Luo, Panwen Tian, Yue Wang, Heng Xu, Lu Chen, Chao Tang, Yang Shu, Shouyue Zhang, Zhoufeng Wang, Jun Zhang, Li Zhang, Lili Jiang, Lunxu Liu, Guowei Che, Chenglin Guo, Hong Zhang, Jiali Wang, Weimin Li
Non-small-cell lung cancer (NSCLC) has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. While never-smoker patients with NSCLC have been well studied through next generation sequencing, we have yet to recognize the potentially unique molecular features of young never-smoker patients with NSCLC. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients, who were diagnosed with lung adenocarcinoma (LUAD) at 45 years or younger...
April 18, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29608557/a-high-throughput-functional-screen-of-human-body-mass-index-gwas-loci-using-tissue-specific-rnai-drosophila-melanogaster-crosses
#6
Thomas J Baranski, Aldi T Kraja, Jill L Fink, Mary Feitosa, Petra A Lenzini, Ingrid B Borecki, Ching-Ti Liu, L Adrienne Cupples, Kari E North, Michael A Province
Human GWAS of obesity have been successful in identifying loci associated with adiposity, but for the most part, these are non-coding SNPs whose function, or even whose gene of action, is unknown. To help identify the genes on which these human BMI loci may be operating, we conducted a high throughput screen in Drosophila melanogaster. Starting with 78 BMI loci from two recently published GWAS meta-analyses, we identified fly orthologs of all nearby genes (± 250KB). We crossed RNAi knockdown lines of each gene with flies containing tissue-specific drivers to knock down (KD) the expression of the genes only in the brain and the fat body...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29363864/srr-intronic-variation-inhibits-expression-of-its-neighbouring-smg6-gene-and-protects-against-temporal-lobe-epilepsy
#7
Hua Tao, Xu Zhou, Qian Xie, Zhonghua Ma, Fuhai Sun, Lili Cui, Yujie Cai, Guoda Ma, Jiawu Fu, Zhou Liu, You Li, Haihong Zhou, Jianghao Zhao, Yanyan Chen, Hui Mai, Ying Chen, Jun Chen, Wei Qi, Chaowen Sun, Bin Zhao, Keshen Li
D-serine is a predominant N-methyl-D-aspartate receptor co-agonist with glutamate, and excessive activation of the receptor plays a substantial role in epileptic seizures. Serine racemase (SRR) is responsible for transforming L-serine to D-serine. In this study, we aimed to investigate the genetic roles of SRR and a neighbouring gene, nonsense-mediated mRNA decay factor (SMG6), in temporal lobe epilepsy (TLE). Here, a total of 496 TLE patients and 528 healthy individuals were successfully genotyped for three SRR tag single nucleotide polymorphisms...
March 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29348139/dissecting-the-functions-of-smg5-smg7-and-pnrc2-in-nonsense-mediated-mrna-decay-of-human-cells
#8
Pamela Nicholson, Asimina Gkratsou, Christoph Josi, Martino Colombo, Oliver Mühlemann
The term "nonsense-mediated mRNA decay" (NMD) originally described the degradation of mRNAs with premature translation-termination codons (PTCs), but its meaning has recently been extended to be a translation-dependent post-transcriptional regulator of gene expression affecting 3%-10% of all mRNAs. The degradation of NMD target mRNAs involves both exonucleolytic and endonucleolytic pathways in mammalian cells. While the latter is mediated by the endonuclease SMG6, the former pathway has been reported to require a complex of SMG5-SMG7 or SMG5-PNRC2 binding to UPF1...
April 2018: RNA
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
#9
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 remains elusive. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3' fragment capture and degradome sequencing...
August 2017: RNA
https://www.readbyqxmd.com/read/28059143/influence-of-coronary-artery-disease-and-subclinical-atherosclerosis-related-polymorphisms-on-the-risk-of-atherosclerosis-in-rheumatoid-arthritis
#10
Raquel López-Mejías, Alfonso Corrales, Esther Vicente, Montserrat Robustillo-Villarino, Carlos González-Juanatey, Javier Llorca, Fernanda Genre, Sara Remuzgo-Martínez, Trinidad Dierssen-Sotos, José A Miranda-Filloy, Marco A Ramírez Huaranga, Trinitario Pina, Ricardo Blanco, Juan J Alegre-Sancho, Enrique Raya, Verónica Mijares, Begoña Ubilla, Iván Ferraz-Amaro, Carmen Gómez-Vaquero, Alejandro Balsa, Francisco J López-Longo, Patricia Carreira, Isidoro González-Álvaro, J Gonzalo Ocejo-Vinyals, Luis Rodríguez-Rodríguez, Benjamín Fernández-Gutiérrez, Santos Castañeda, Javier Martín, Miguel A González-Gay
A genetic component influences the development of atherosclerosis in the general population and also in rheumatoid arthritis (RA). However, genetic polymorphisms associated with atherosclerosis in the general population are not always involved in the development of cardiovascular disease (CVD) in RA. Accordingly, a study in North-American RA patients did not show the association reported in the general population of coronary artery disease with a series of relevant polymorphisms (TCF21, LPA, HHIPL1, RASD1-PEMT, MRPS6, CYP17A1-CNNM2-NT5C2, SMG6-SRR, PHACTR1, WDR12 and COL4A1-COL4A2)...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27864472/transcriptome-wide-identification-of-nmd-targeted-human-mrnas-reveals-extensive-redundancy-between-smg6-and-smg7-mediated-degradation-pathways
#11
Martino Colombo, Evangelos D Karousis, Joël Bourquin, Rémy Bruggmann, Oliver Mühlemann
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6, and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors...
February 2017: RNA
https://www.readbyqxmd.com/read/27754159/os-30-05-genetic-risk-score-determines-dipping-profile-in-patients-with-coronary-heart-disease
#12
Marcin Wirtwein, Olle Melander, Marketa Sjogren, Michal Hoffmann, Marcin Gruchala, Wojciech Sobiczewski
OBJECTIVE: The aim of this study is to report the relationship between certain single nucleotide polymorphisms (SNP) and blunted nighttime blood pressure (BP) fall in hypertensive patients with CAD confirmed by coronary angiography. DESIGN AND METHOD: According to the percentage decrease in mean systolic (SBP) and diastolic BP (DBP) during the nighttime period subjects were classified as dippers or non-dippers (nighttime relative SBP or DBP decline ≥ and <10% respectively)...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27693585/cleavage-of-influenza-rna-by-using-a-human-puf-based-artificial-rna-binding-protein-staphylococcal-nuclease-hybrid
#13
Tomoaki Mori, Kento Nakamura, Keisuke Masaoka, Yusuke Fujita, Ryosuke Morisada, Koichi Mori, Takamasa Tobimatsu, Takashi Sera
Various viruses infect animals and humans and cause a variety of diseases, including cancer. However, effective methodologies to prevent virus infection have not yet been established. Therefore, development of technologies to inactivate viruses is highly desired. We have already demonstrated that cleavage of a DNA virus genome was effective to prevent its replication. Here, we expanded this methodology to RNA viruses. In the present study, we used staphylococcal nuclease (SNase) instead of the PIN domain (PilT N-terminus) of human SMG6 as an RNA-cleavage domain and fused the SNase to a human Pumilio/fem-3 binding factor (PUF)-based artificial RNA-binding protein to construct an artificial RNA restriction enzyme with enhanced RNA-cleavage rates for influenzavirus...
October 28, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27643089/os-30-05-genetic-risk-score-determines-dipping-profile-in-patients-with-coronary-heart-disease
#14
Marcin Wirtwein, Olle Melander, Marketa Sjogren, Michal Hoffmann, Marcin Gruchala, Wojciech Sobiczewski
OBJECTIVE: The aim of this study is to report the relationship between certain single nucleotide polymorphisms (SNP) and blunted nighttime blood pressure (BP) fall in hypertensive patients with CAD confirmed by coronary angiography. DESIGN AND METHOD: According to the percentage decrease in mean systolic (SBP) and diastolic BP (DBP) during the nighttime period subjects were classified as dippers or non-dippers (nighttime relative SBP or DBP decline ≥ and <10% respectively)...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27189819/the-relationship-between-gene-polymorphisms-and-dipping-profile-in-patients-with-coronary-heart-disease
#15
Marcin Wirtwein, Olle Melander, Marketa Sjőgren, Michal Hoffmann, Krzysztof Narkiewicz, Marcin Gruchala, Wojciech Sobiczewski
BACKGROUND: The aim of this study is to report the relationship between certain single-nucleotide polymorphisms (SNPs) and blunted nighttime blood pressure (BP) fall in patients with coronary artery disease confirmed by coronary angiography. METHODS: According to the percentage decrease in mean systolic BP (SBP) and diastolic BP (DBP) during the nighttime period, subjects were classified as dippers or nondippers (nighttime relative SBP or DBP decline ≥10% and <10%, respectively)...
September 2016: American Journal of Hypertension
https://www.readbyqxmd.com/read/26821332/genetic-burden-analyses-of-phenotypes-relevant-to-aging-in-the-berlin-aging-study-ii-base-ii
#16
Christina M Lill, Tian Liu, Kristina Norman, Antje Meyer, Elisabeth Steinhagen-Thiessen, Ilja Demuth, Lars Bertram
BACKGROUND: Body mass index (BMI), bone mineral density (BMD), and telomere length are phenotypes that modulate the course of aging. Over 40% of their phenotypic variance is determined by genetics. Genome-wide association studies (GWAS) have recently uncovered >100 independent single-nucleotide polymorphisms (SNPs) showing genome-wide significant (p < 5 × 10-8) association with these traits. OBJECTIVE: To test the individual and combined impact of previously reported GWAS SNPs on BMI, BMD, and relative leukocyte telomere length (rLTL) in ∼1,750 participants of the Berlin Aging Study II (BASE-II), a cohort consisting predominantly of individuals >60 years of age...
2016: Gerontology
https://www.readbyqxmd.com/read/26442679/unique-aspects-of-plant-nonsense-mediated-mrna-decay
#17
REVIEW
Orit Shaul
Nonsense-mediated mRNA Decay (NMD) is a eukaryotic quality-control mechanism that governs the stability of both aberrant and normal transcripts. Although plant and mammalian NMD share great similarity, they differ in certain mechanistic and regulatory aspects. Whereas SMG6 (from Caenorhabditis elegans 'suppressor with morphogenetic effect on genitalia')-catalyzed endonucleolytic cleavage is a prominent step in mammalian NMD, plant NMD targets are degraded by an SMG7-induced exonucleolytic pathway. Both mammalian and plant NMD are downregulated by stress, thereby enhancing the expression of defense response genes...
November 2015: Trends in Plant Science
https://www.readbyqxmd.com/read/26015811/tobacco-smoking-is-associated-with-methylation-of-genes-related-to-coronary-artery-disease
#18
Rebecca V Steenaard, Symen Ligthart, Lisette Stolk, Marjolein J Peters, Joyce B van Meurs, Andre G Uitterlinden, Albert Hofman, Oscar H Franco, Abbas Dehghan
BACKGROUND: Tobacco smoking, a risk factor for coronary artery disease (CAD), is known to modify DNA methylation. We hypothesized that tobacco smoking modifies methylation of the genes identified for CAD by genome-wide association study (GWAS). RESULTS: We selected genomic regions based on 150 single-nucleotide polymorphisms (SNPs) identified in the largest GWAS on CAD. We investigated the association between current smoking and the CpG sites within and near these CAD-related genes...
2015: Clinical Epigenetics
https://www.readbyqxmd.com/read/25770585/smg6-est1-licenses-embryonic-stem-cell-differentiation-via-nonsense-mediated-mrna-decay
#19
Tangliang Li, Yue Shi, Pei Wang, Luis Miguel Guachalla, Baofa Sun, Tjard Joerss, Yu-Sheng Chen, Marco Groth, Anja Krueger, Matthias Platzer, Yun-Gui Yang, Karl Lenhard Rudolph, Zhao-Qi Wang
Nonsense-mediated mRNA decay (NMD) is a post-transcriptional mechanism that targets aberrant transcripts and regulates the cellular RNA reservoir. Genetic modulation in vertebrates suggests that NMD is critical for cellular and tissue homeostasis, although the underlying mechanism remains elusive. Here, we generate knockout mice lacking Smg6/Est1, a key nuclease in NMD and a telomerase cofactor. While the complete loss of Smg6 causes mouse lethality at the blastocyst stage, inducible deletion of Smg6 is compatible with embryonic stem cell (ESC) proliferation despite the absence of telomere maintenance and functional NMD...
June 12, 2015: EMBO Journal
https://www.readbyqxmd.com/read/25429978/identification-of-smg6-cleavage-sites-and-a-preferred-rna-cleavage-motif-by-global-analysis-of-endogenous-nmd-targets-in-human-cells
#20
Skye A Schmidt, Patricia L Foley, Dong-Hoon Jeong, Linda A Rymarquis, Francis Doyle, Scott A Tenenbaum, Joel G Belasco, Pamela J Green
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...
January 2015: Nucleic Acids Research
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