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https://www.readbyqxmd.com/read/28929622/endonuclease-regnase-1-monocyte-chemotactic-protein-1-induced-protein-1-mcpip1-in-controlling-immune-responses-and-beyond
#1
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/28928834/cd55-and-cd59-expression-protects-her2-overexpressing-breast-cancer-cells-from-trastuzumab-induced-complement-dependent-cytotoxicity
#2
Yu Wang, Ya-Jun Yang, Zhu Wang, Juan Liao, Mei Liu, Xiao-Rong Zhong, Hong Zheng, Yan-Ping Wang
A large proportion (40-60%) of patients with human epidermal growth factor receptor 2 (HER2)-overexpressing breast cancer do not benefit from trastuzumab treatment, potentially due to the lack of complement-dependent cytotoxicity (CDC) activation. In the present study, the effect of complement decay-accelerating factor (CD55) and CD59 glycoprotein precursor (CD59) expression on trastuzumab-induced CDC in HER2-positive breast cancer cell lines was investigated. The CD55 and CD59-overexpressing and HER2-positive cell lines SK-BR-3 and BT474 were selected for subsequent experiments...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28927531/discriminating-rna-variants-with-single-molecule-allele-specific-fish
#3
REVIEW
Martyna O Urbanek, Wlodzimierz J Krzyzosiak
DNA mutations of various types often affect the cellular localization and function of gene products. The role of mutant transcripts in the pathogenesis of human disease is increasingly recognized. Among the pathogenic RNA variants are transcripts with single nucleotide substitutions, small insertions or deletions, aberrantly or alternatively spliced transcripts and RNAs derived from fused genes. To discriminate among transcripts, particularly those of low abundance, showing small or large sequence differences, a highly sensitive and specific RNA imaging method is required...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28923956/arabidopsis-m-6-a-demethylase-activity-modulates-viral-infection-of-a-plant-virus-and-the-m-6-a-abundance-in-its-genomic-rnas
#4
Mireya Martínez-Pérez, Frederic Aparicio, Maria Pilar López-Gresa, Jose María Bellés, Jesus A Sánchez-Navarro, Vicente Pallás
N(6)-methyladenosine (m(6)A) is an internal, reversible nucleotide modification that constitutes an important regulatory mechanism in RNA biology. Unlike mammals and yeast, no component of the m(6)A cellular machinery has been described in plants at present. m(6)A has been identified in the genomic RNAs of diverse mammalian viruses and, additionally, viral infection was found to be modulated by the abundance of m(6)A in viral RNAs. Here we show that the Arabidopsis thaliana protein atALKBH9B (At2g17970) is a demethylase that removes m(6)A from single-stranded RNA molecules in vitro...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28917839/m2b-macrophage-polarization-accompanied-with-reduction-of-long-noncoding-rna-gas5
#5
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
#6
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
#7
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/28881683/inhibition-of-cox2-enhances-the-chemosensitivity-of-dichloroacetate-in-cervical-cancer-cells
#8
Bo Li, Xinzhe Li, Haojun Xiong, Peng Zhou, Zhenhong Ni, Teng Yang, Yan Zhang, Yijun Zeng, Jintao He, Fan Yang, Nan Zhang, Yuting Wang, Yingru Zheng, Fengtian He
Dichloroacetate (DCA), a traditional mitochondria-targeting agent, has shown promising prospect as a sensitizer in fighting against malignancies including cervical cancer. But it is unclear about the effect of DCA alone on cervical tumor. Moreover, previous reports have demonstrated that the increased cyclooxygenase-2 (COX2) expression is associated with chemoresistance and poor prognosis of cervical cancer. However, it is still unknown whether COX2 can affect the sensitivity of DCA in cervical cancer cells...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28878343/plasmid-transfection-influences-the-readout-of-nonsense-mediated-mrna-decay-reporter-assays-in-human-cells
#9
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/28877997/the-pumilio-domain-protein-puf6-contributes-to-sider2-retroposon-mediated-mrna-decay-in-leishmania
#10
Hiva Azizi, Carole Dumas, Barbara Papadopoulou
Leishmania and other trypanosomatid protozoa lack control at the level of transcription initiation and regulate gene expression exclusively posttranscriptionally. We have reported previously that Leishmania harbors a unique class of Short Interspersed DEgenerate Retroposons (SIDERs) that are predominantly located within 3'UTRs and play a major role in posttranscriptional control. We have shown that members of the SIDER2 subfamily initiate mRNA decay through endonucleolytic cleavage within the second conserved 79-nt signature sequence of SIDER2 retroposons...
September 6, 2017: RNA
https://www.readbyqxmd.com/read/28877986/phosphorylation-and-nuclear-transit-modulate-the-balance-between-normal-function-and-terminal-aggregation-of-the-yeast-rna-binding-protein-ssd1
#11
Cornelia Kurischko, James R Broach
Yeast Ssd1 is an RNA-binding protein that shuttles between the nucleus and cytoplasm. Ssd1 interacts with its target mRNAs initially during transcription by binding through its N-terminal prion-like domain (PLD) to the C-terminal domain of RNA polymerase II. Ssd1 subsequently targets mRNAs acquired in the nucleus either to daughter cells for translation or to stress granules (SG) and P-bodies (PB) for mRNA storage or decay. Here we show that PB components assist in the nuclear export of Ssd1and subsequent targeting of Ssd1 to PB sites in the cytoplasm...
September 6, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28877463/mpp6-incorporation-in-the-nuclear-exosome-contributes-to-rna-channeling-through-the-mtr4-helicase
#12
Sebastian Falk, Fabien Bonneau, Judith Ebert, Alexander Kögel, Elena Conti
The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9-Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Biochemical and structural studies to date have shed insights into the mechanisms of the exosome core and its nuclear cofactors, with the exception of Mpp6. We report the 3.2-Å resolution crystal structure of a S. cerevisiae Exo-9-Mpp6 complex, revealing how linear motifs in the Mpp6 middle domain bind Rrp40 via evolutionary conserved residues...
September 5, 2017: Cell Reports
https://www.readbyqxmd.com/read/28875934/me31b-globally-represses-maternal-mrnas-by-two-distinct-mechanisms-during-the-drosophila-maternal-to-zygotic-transition
#13
Miranda Wang, Michael Ly, Andrew Lugowski, John D Laver, Howard D Lipshitz, Craig A Smibert, Olivia S Rissland
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). We show that the RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay...
September 6, 2017: ELife
https://www.readbyqxmd.com/read/28874147/assessing-the-activity-of-nonsense-mediated-mrna-decay-in-lung-cancer
#14
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/28869969/m-6-a-modulates-haematopoietic-stem-and-progenitor-cell-specification
#15
Chunxia Zhang, Yusheng Chen, Baofa Sun, Lu Wang, Ying Yang, Dongyuan Ma, Junhua Lv, Jian Heng, Yanyan Ding, Yuanyuan Xue, Xinyan Lu, Wen Xiao, Yun-Gui Yang, Feng Liu
N(6)-methyladenosine (m(6)A) has been identified as the most abundant modification on eukaryote messenger RNA (mRNA). Although the rapid development of high-throughput sequencing technologies has enabled insight into the biological functions of m(6)A modification, the function of m(6)A during vertebrate embryogenesis remains poorly understood. Here we show that m(6)A determines cell fate during the endothelial-to-haematopoietic transition (EHT) to specify the earliest haematopoietic stem/progenitor cells (HSPCs) during zebrafish embryogenesis...
September 14, 2017: Nature
https://www.readbyqxmd.com/read/28866468/topical-silver-diamine-fluoride-for-dental-caries-arrest-in-preschool-children-a-randomized-controlled-trial-and-microbiological-analysis-of-caries-associated-microbes-and-resistance-gene-expression
#16
Peter Milgrom, Jeremy A Horst, Sharity Ludwig, Marilynn Rothen, Benjamin W Chaffee, Svetlana Lyalina, Katherine S Pollard, Joseph L DeRisi, Lloyd Mancl
OBJECTIVES: The Stopping Cavities Trial investigated effectiveness and safety of 38% silver diamine fluoride in arresting caries lesions. MATERIALS AND METHODS: The study was a double-blind randomized placebo-controlled superiority trial with 2 parallel groups. The sites were Oregon preschools. Sixty-six preschool children with ≥1 lesion were enrolled. Silver diamine fluoride (38%) or placebo (blue-tinted water), applied topically to the lesion. The primary endpoint was caries arrest (lesion inactivity, Nyvad criteria) 14-21days post intervention...
August 30, 2017: Journal of Dentistry
https://www.readbyqxmd.com/read/28859318/effect-of-the-rna-pyrophosphohydrolase-rpph-on-envelope-integrity-in-escherichia-coli
#17
Umji Choi, Young-Ha Park, Yeon-Ran Kim, Yeong-Jae Seok, Chang-Ro Lee
The bacterial enzyme RppH initiates mRNA decay by removing pyrophosphate from 5΄-triphosphorylated mRNA. Escherichia coli RppH has promiscuous substrate specificity, but relatively few transcripts are affected by loss of RppH. The phenotypic analysis of the rppH mutant is required for understanding the physiological role of RppH, but the phenotype of the rppH mutant has not yet been determined. In this study, we provide several phenotypes of the rppH mutant associated with envelope integrity. Through phenotype analysis and drug susceptibility testing, we found that the rppH mutant is sensitive to a variety of chemicals including antibiotics, and is also significantly sensitive to envelope stresses, such as osmotic stress, ethanol and sodium dodecyl sulfate...
August 15, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28851853/translational-repression-of-the-rpos-antiadapter-irad-by-csra-is-mediated-via-translational-coupling-to-a-short-upstream-open-reading-frame
#18
Hongmarn Park, Louise C McGibbon, Anastasia H Potts, Helen Yakhnin, Tony Romeo, Paul Babitzke
CsrA is a global regulatory RNA binding protein that has important roles in regulating carbon metabolism, motility, biofilm formation, and numerous other cellular processes. IraD functions as an antiadapter protein that inhibits RssB-mediated degradation of RpoS, the general stress response and stationary-phase sigma factor of Escherichia coli Here we identified a novel mechanism in which CsrA represses iraD translation via translational coupling. Expression studies with quantitative reverse transcriptase PCR, Western blotting, and lacZ fusions demonstrated that CsrA represses iraD expression...
August 29, 2017: MBio
https://www.readbyqxmd.com/read/28840253/interaction-and-cross-talk-between-non-coding-rnas
#19
REVIEW
Soichiro Yamamura, Mitsuho Imai-Sumida, Yuichiro Tanaka, Rajvir Dahiya
Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors...
August 24, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28834196/advanced-cell-based-modeling-of-the-royal-disease-characterization-of-the-mutated-f9-mrna
#20
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
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