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Nonsense-mediated mRNA decay

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https://www.readbyqxmd.com/read/29036709/deep-learning-of-the-splicing-epi-genetic-code-reveals-a-novel-candidate-mechanism-linking-histone-modifications-to-esc-fate-decision
#1
Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29034140/regulation-of-gene-expression-by-translation-factor-eif5a-hypusine-modified-eif5a-enhances-nonsense-mediated-mrna-decay-in-human-cells
#2
Mainul Hoque, Ji Yeon Park, Yun-Juan Chang, Augusto D Luchessi, Tavane D Cambiaghi, Raghavendra Shamanna, Hartmut M Hanauske-Abel, Bart Holland, Tsafi Pe'ery, Bin Tian, Michael B Mathews
Nonsense-mediated mRNA decay (NMD) couples protein synthesis to mRNA turnover. It eliminates defective transcripts and controls the abundance of certain normal mRNAs. Our study establishes a connection between NMD and the translation factor eIF5A (eukaryotic initiation factor 5A) in human cells. eIF5A modulates the synthesis of groups of proteins (the eIF5A regulon), and undergoes a distinctive two-step post-translational modification (hypusination) catalyzed by deoxyhypusine synthase and deoxyhypusine hydroxylase...
2017: Translation
https://www.readbyqxmd.com/read/29020934/transcriptome-analyses-reveal-sr45-to-be-a-neutral-splicing-regulator-and-a-suppressor-of-innate-immunity-in-arabidopsis-thaliana
#3
Xiao-Ning Zhang, Yifei Shi, Jordan J Powers, Nikhil B Gowda, Chong Zhang, Heba M M Ibrahim, Hannah B Ball, Samuel L Chen, Hua Lu, Stephen M Mount
BACKGROUND: Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regulatory proteins and spliceosomal subunits. Although SR45 has orthologs in diverse eukaryotes, including human RNPS1, the sr45-1 null mutant is viable. Narrow flower petals and reduced seed formation suggest that SR45 regulates genes involved in diverse processes, including reproduction...
October 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28984438/engineering-the-genetic-code-in-cells-and-animals-biological-considerations-and-impacts
#4
Lei Wang
Expansion of the genetic code allows unnatural amino acids (Uaas) to be site-specifically incorporated into proteins in live biological systems, thus enabling novel properties selectively introduced into target proteins in vivo for basic biological studies and for engineering of novel biological functions. Orthogonal components including tRNA and aminoacyl-tRNA synthetase (aaRS) are expressed in live cells to decode a unique codon (often the amber stop codon UAG) as the desired Uaa. Initially developed in E...
October 6, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28983119/the-gbap1-pseudogene-acts-as-a-cerna-for-the-glucocerebrosidase-gene-gba-by-sponging-mir-22-3p
#5
Letizia Straniero, Valeria Rimoldi, Maura Samarani, Stefano Goldwurm, Alessio Di Fonzo, Rejko Krüger, Michela Deleidi, Massimo Aureli, Giulia Soldà, Stefano Duga, Rosanna Asselta
Mutations in the GBA gene, encoding lysosomal glucocerebrosidase, represent the major predisposing factor for Parkinson's disease (PD), and modulation of the glucocerebrosidase activity is an emerging PD therapy. However, little is known about mechanisms regulating GBA expression. We explored the existence of a regulatory network involving GBA, its expressed pseudogene GBAP1, and microRNAs. The high level of sequence identity between GBA and GBAP1 makes the pseudogene a promising competing-endogenous RNA (ceRNA), functioning as a microRNA sponge...
October 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28977534/fractionation-iclip-detects-persistent-sr-protein-binding-to-conserved-retained-introns-in-chromatin-nucleoplasm-and-cytoplasm
#6
Mattia Brugiolo, Valentina Botti, Na Liu, Michaela Müller-McNicoll, Karla M Neugebauer
RNA binding proteins (RBPs) regulate the lives of all RNAs from transcription, processing, and function to decay. How RNA-protein interactions change over time and space to support these roles is poorly understood. Towards this end, we sought to determine how two SR proteins-SRSF3 and SRSF7, regulators of pre-mRNA splicing, nuclear export and translation-interact with RNA in different cellular compartments. To do so, we developed Fractionation iCLIP (Fr-iCLIP), in which chromatin, nucleoplasmic and cytoplasmic fractions are prepared from UV-crosslinked cells and then subjected to iCLIP...
August 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28959040/endoplasmic-reticulum-stress-preconditioning-modifies-intracellular-mercury-content-by-upregulating-membrane-transporters
#7
Fusako Usuki, Masatake Fujimura, Akio Yamashita
Endoplasmic reticulum (ER) stress preconditioning protects cells against methylmercury (MeHg) cytotoxicity by inducing integrated stress responses such as eIF2α phosphorylation, ATF4 accumulation, and nonsense-mediated mRNA decay (NMD) suppression. Here we demonstrated that ER stress preconditioning results in the upregulation of membrane transporters, leading to a decrease in intracellular mercury content. Our analyses showed that ER stress preconditioning upregulated the expression of methionine transporters that affect the cellular influx of MeHg, LAT1, LAT3, and SNAT2; and a membrane transporter that affects the efflux of MeHg, ABCC4, in MeHg-susceptible myogenic cells...
September 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28950212/p-val19glyfs-21-and-p-leu228-variants-in-the-survival-of-motor-neuron-1-trigger-nonsense-mediated-mrna-decay-causing-the-smn1-ptc-transcripts-degradation
#8
Yu-Jin Qu, Lin Ge, Jin-Li Bai, Yan-Yan Cao, Yu-Wei Jin, Hong Wang, Lan Yang, Fang Song
Spinal Muscular Atrophy (SMA) results from loss-of-function mutations in the survival of motor neuron 1 (SMN1) gene. Our previous research showed that 40% of variants were nonsense or frameshift variants and SMN1 mRNA levels in the patients carrying these variants were significantly decreased. Here we selected one rare variant (p.Val19Glyfs*21) and one common variant (p.Leu228*) to explore the degradation mechanism of mutant transcripts. The levels of full-length (FL)-SMN1 transcripts and SMN protein in the cell lines from the patients with these variants were both significantly reduced (p<0...
September 15, 2017: Mutation Research
https://www.readbyqxmd.com/read/28944923/-corrigendum-nonsense-mediated-mrna-decay-factor-upf2-exists-in-both-the-nucleoplasm-and-the-cytoplasm
#9
Takanori Tatsuno, Yuka Nakamura, Shaofu Ma, Naohisa Tomosugi, Yasuhito Ishigaki
Following the publication of this article, after having re-examined our manuscript, an error was noted in the Acknowledgments section regarding the funding of our study. The Acknowledgments section should have appeared as follows: "This work was supported by grants from the Kanazawa Medical University (nos. C2014-3, C2015-1 and S2014-15), a grant from the Strategic Research Project (no. H2012-16 [S1201022]) from Kanazawa Medical University, Ministry of Education, Culture, Sports, Science and Technology, Japan (KAKENHI no...
September 25, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28942451/the-human-rna-surveillance-factor-upf1-modulates-gastric-cancer-progression-by-targeting-long-non-coding-rna-malat1
#10
Li Li, Yingying Geng, Ru Feng, Qinqin Zhu, Bei Miao, Jiang Cao, Sujuan Fei
BACKGROUND/AIMS: The long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is overexpressed in numerous cancers. However, whether MALAT1 is regulated and the related mechanisms in gastric cancer remain unclear. METHODS: Immunohistochemistry and qRT-PCR analyses were used to detect the expression levels of UPF1 and MALAT1 in gastric cancer and adjacent normal tissues. MTT, cell cycle, apoptosis and transwell assays were performed to examine the effects of UPF1 on cell cycle progression, cell proliferation, apoptosis, migration and invasion...
2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28937992/efficient-generation-of-mutations-mediated-by-crispr-cas9-in-the-hairy-root-transformation-system-of-brassica-carinata
#11
Thomas W Kirchner, Markus Niehaus, Thomas Debener, Manfred K Schenk, Marco Herde
A protocol for the induction of site-directed deletions and insertions in the genome of Brassica carinata with CRISPR is described. The construct containing the Cas9 nuclease and the guide RNA (gRNA) was delivered by the hairy root transformation technique, and a successful transformation was monitored by GFP fluorescence. PAGE analysis of an amplified region, presumably containing the deletions and insertions, demonstrated up to seven different indels in one transgenic root and in all analyzed roots a wildtype allele of the modified gene was not detectable...
2017: PloS One
https://www.readbyqxmd.com/read/28934391/homozygous-kidins220-loss-of-function-variants-in-fetuses-with-cerebral-ventriculomegaly-and-limb-contractures
#12
I-L Mero, H H Mørk, Y Sheng, A Blomhoff, G L Opheim, Aa Erichsen, M D Vigeland, K K Selmer
Heterozygous mutations in KIDINS220 were recently suggested a cause of spastic paraplegia, intellectual disability, nystagmus and obesity. All patients carried terminal nonsense de novo mutations that seemed to escape nonsense-mediated mRNA decay. The mechanism for pathogenicity is yet unexplained, as it seems that heterozygous loss-of-function variants of KIDINS220 are generally well tolerated. We present a consanguineous couple who experienced four pregnancy terminations due to repeated findings in the fetuses comprising enlarged cerebral ventricles and limb contractures...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28929622/endonuclease-regnase-1-monocyte-chemotactic-protein-1-induced-protein-1-mcpip1-in-controlling-immune-responses-and-beyond
#13
REVIEW
Osamu Takeuchi
The activation of inflammatory cells is controlled at transcriptional and posttranscriptional levels. Posttranscriptional regulation modifies mRNA stability and translation, allowing for elaborate control of proteins required for inflammation, such as proinflammatory cytokines, prostaglandin synthases, cell surface co-stimulatory molecules, and even transcriptional modifiers. Such regulation is important for coordinating the initiation and resolution of inflammation, and is mediated by a set of RNA-binding proteins (RBPs), including Regnase-1, Roquin, Tristetraprolin (TTP), and AU-rich elements/poly(U)-binding/degradation factor 1 (AUF1)...
September 20, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28899899/dual-function-of-upf3b-in-early-and-late-translation-termination
#14
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...
October 16, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28894297/the-pnkd-gene-is-associated-with-tourette-disorder-or-tic-disorder-in-a-multiplex-family
#15
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/28878343/plasmid-transfection-influences-the-readout-of-nonsense-mediated-mrna-decay-reporter-assays-in-human-cells
#16
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
#17
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
#18
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
#19
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
#20
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
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