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https://www.readbyqxmd.com/read/28642780/rrp42-a-subunit-of-exosome-plays-an-important-role-in-female-gametophytes-development-and-mesophyll-cell-morphogenesis-in-arabidopsis
#1
Xiaoyuan Yan, Zongyun Yan, Yuzhen Han
The exosome complex plays a central and essential role in RNA metabolism. However, current research on functions of exosome subunit in plants is limited. Here, we used an egg cell-specific promoter-controlled CRISPR/Cas9 system to knock out RRP42 which encodes a core subunit of the Arabidopsis exosome and presented evidence that RRP42 is essential for the development of female gametophytes. Next, we designed three different amiRNAs targeting RRP42. The rrp42 knock-down mutants mainly displayed variegated and serrated leaves, especially in cauline leaves...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642749/rna-seq-reveals-enhanced-sugar-metabolism-in-streptococcus-mutans-co-cultured-with-candida-albicans-within-mixed-species-biofilms
#2
Jinzhi He, Dongyeop Kim, Xuedong Zhou, Sang-Joon Ahn, Robert A Burne, Vincent P Richards, Hyun Koo
Early childhood caries (ECC), which can lead to rampant tooth-decay that is painful and costly to treat, is one of the most prevalent infectious diseases affecting children worldwide. Previous studies support that interactions between Streptococcus mutans and Candida albicans are associated with the pathogenesis of ECC. The presence of Candida enhances S. mutans growth, fitness and accumulation within biofilms in vitro, although the molecular basis for these behaviors is undefined. Using an established co-cultivation biofilm model and RNA-Seq, we investigated how C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#3
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28629776/unveiling-the-non-repair-face-of-the-base-excision-repair-pathway-in-rna-processing-a-missing-link-between-dna-repair-and-gene-expression
#4
REVIEW
Giulia Antoniali, Matilde Clarissa Malfatti, Gianluca Tell
The Base Excision Repair (BER) pathway, initially studied as a mere DNA repair pathway, has been later found to be implicated in the expression of cancer related genes in human. For several years, this intricate involvement in apparently different processes represented a mystery, which we now are starting to unveil. The BER handles simple alkylation and oxidative lesions arising from both endogenous and exogenous sources, including cancer therapy agents. Surprisingly, BER pathway involvement in transcriptional regulation, immunoglobulin variability and switch recombination, RNA metabolism and nucleolar function is astonishingly consolidating...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28628654/the-apah-like-phosphatase-tbalph1-is-the-major-mrna-decapping-enzyme-of-trypanosomes
#5
Susanne Kramer
5'-3' decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5'-3' exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5'-3' degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1) as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding...
June 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28624538/analysis-of-mrna-deadenylation-by-multi-protein-complexes
#6
Michael W Webster, James A W Stowell, Terence T L Tang, Lori A Passmore
Poly(A) tails are found at the 3' end of almost every eukaryotic mRNA and are important for the stability of mRNAs and their translation into proteins. Thus, removal of the poly(A) tail, a process called deadenylation, is critical for regulation of gene expression. Most deadenylation enzymes are components of large multi-protein complexes. Here, we describe an in vitro deadenylation assay developed to study the exonucleolytic activities of the multi-protein Ccr4-Not and Pan2-Pan3 complexes. We discuss how this assay can be used with short synthetic RNAs, as well as longer RNA substrates generated using in vitro transcription...
June 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28613834/amino-functionalized-5-cap-analogs-as-tools-for-site-specific-sequence-independent-labeling-of-messenger-rna
#7
Marcin Warminski, Pawel J Sikorski, Zofia Warminska, Maciej Lukaszewicz, Anna Kropiwnicka, Joanna Zuberek, Edward Darzynkiewicz, Joanna Kowalska, Jacek Jemielity
mRNA is a template for protein biosynthesis, and consequently mRNA transport, translation, and turnover are key elements in the overall regulation of gene expression. Along with growing interest in the mechanisms regulating mRNA decay and localization, there is an increasing need for tools enabling convenient fluorescent labelling or affinity tagging of mRNA. We report new mRNA 5' cap analog-based tools that enable site-specific labelling of RNA within the cap using N-hydroxysuccinimide (NHS) chemistry. We explored two complementary methods: a co-transcriptional labelling method, in which the label is first attached to cap analog and then incorporated into RNA by transcription in vitro, and post-transcriptional labelling method, in which an amino-functionalized cap analog is incorporated into RNA followed by chemical labelling of the resulting transcript...
June 14, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28606139/a-loss-of-pdxk-model-of-parkinson-disease-in-drosophila-can-be-suppressed-by-buffy
#8
P Githure M'Angale, Brian E Staveley
BACKGROUND: The identification of a DNA variant in pyridoxal kinase (Pdxk) associated with increased risk to Parkinson disease (PD) gene led us to study the inhibition of this gene in the Dopa decarboxylase (Ddc)-expressing neurons of the well-studied model organism Drosophila melanogaster. The multitude of biological functions attributable to the vitamers catalysed by this kinase reveal an overabundance of possible links to PD, that include dopamine synthesis, antioxidant activity and mitochondrial function...
June 12, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28600326/up-frameshift-protein-upf1-regulates-neurospora-crassa-circadian-and-diurnal-growth-rhythms
#9
Yilan Wu, Yin Zhang, Yunpeng Sun, Jiali Yu, Peiliang Wang, Huan Ma, Shijunyin Chen, Lizhen Ma, Dongyang Zhang, Qun He, Jinhu Guo
Nonsense-mediated RNA decay (NMD) is a crucial post-transcriptional regulatory mechanism that recognizes and eliminates aberrantly processed transcripts, and mediates the expression of normal gene transcripts. In this study, we report that in the filamentous fungus Neurospora crassa, the NMD factors play a conserved role in regulating the surveillance of NMD targets including PTC-containing transcripts and normal transcripts. The circadian rhythms in all of the upf1-3 knockout strains, which are principle NMD factors, were aberrant...
June 9, 2017: Genetics
https://www.readbyqxmd.com/read/28595636/two-novel-c-terminal-frameshift-mutations-in-the-%C3%AE-globin-gene-lead-to-rapid-mrna-decay
#10
Katarzyna Rawa, Roman J Szczesny, Ewelina P Owczarek, Anna Adamowicz-Salach, Anna Klukowska, Urszula Demkow, Danuta Plochocka, Pawel Szczesny, Monika Gora, Andrzej Dziembowski, Beata Burzynska
BACKGROUND: The thalassemia syndromes are classified according to the globin chain or chains whose production is affected. β-thalassemias are caused by point mutations or, more rarely, deletions or insertions of a few nucleotides in the β-globin gene or its immediate flanking sequences. These mutations interfere with the gene function either at the transcriptional, translational or posttranslational level. METHODS: Two cases of Polish patients with hereditary hemolytic anemia suspected of thalassemia were studied...
June 8, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28592548/evaluation-of-the-aptima-hiv-1-quant-dx-assay-for-hiv-1-rna-quantitation-in-different-biological-specimen-types
#11
Christina Yek, Marta Massanella, Tashi Peling, Kristen Lednovich, Sangeetha V Nair, Andrew Worlock, Milenka Vargas, Sara Gianella, Ronald J Ellis, Matthew C Strain, Michael P Busch, C Thomas Nugent, Douglas D Richman
Background The search for a cure for HIV infection has highlighted the need for increasingly sensitive and precise assays to measure viral burden in various tissues and body fluids. We describe the application of a standardized assay for HIV-1 RNA in multiple specimen types.Methods The fully automated Aptima HIV-1 Quant Dx assay (Aptima assay) is FDA-cleared for blood plasma HIV-1 RNA quantitation. In this study, the Aptima assay was applied for the quantitation of HIV RNA in peripheral blood mononuclear cells (PBMC; n=72), seminal plasma (n=20), cerebrospinal fluid (CSF; n=36), dried blood spots (DBS; n=104) and dried plasma spots (DPS; n=104)...
June 7, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28586478/autoregulation-of-rbm10-and-cross-regulation-of-rbm10-rbm5-via-alternative-splicing-coupled-nonsense-mediated-decay
#12
Yue Sun, Yufang Bao, Wenjian Han, Fan Song, Xianfeng Shen, Jiawei Zhao, Ji Zuo, David Saffen, Wei Chen, Zefeng Wang, Xintian You, Yongbo Wang
Mutations in the spliceosomal RNA binding protein RBM10 cause TARP syndrome and are frequently observed in lung adenocarcinoma (LUAD). We have previously shown that RBM10 enhances exon skipping of its target genes, including its paralog RBM5. Here, we report that RBM10 negatively regulates its own mRNA and protein expression and that of RBM5 by promoting alternative splicing-coupled nonsense-mediated mRNA decay (AS-NMD). Through computational analysis and experimental validation, we identified RBM10-promoted skipping of exon 6 or 12 in RBM10 and exon 6 or 16 in RBM5 as the underlying AS-NMD events...
June 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28581511/rna-fate-determination-through-cotranscriptional-adenosine-methylation-and-microprocessor-binding
#13
Philip Knuckles, Sarah H Carl, Michael Musheev, Christof Niehrs, Alice Wenger, Marc Bühler
Eukaryotic gene expression is heavily regulated at the transcriptional and post-transcriptional levels. An additional layer of regulation occurs co-transcriptionally through processing and decay of nascent transcripts physically associated with chromatin. This process involves RNA interference (RNAi) machinery and is well documented in yeast, but little is known about its conservation in mammals. Here we show that Dgcr8 and Drosha physically associate with chromatin in murine embryonic stem cells (mES), specifically with a subset of transcribed coding and noncoding genes...
June 5, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28575439/mediator-binds-to-boundaries-of-chromosomal-interaction-domains-and-to-proteins-involved-in-dna-looping-rna-metabolism-chromatin-remodeling-and-actin-assembly
#14
Razvan V Chereji, Vasudha Bharatula, Nils Elfving, Jeanette Blomberg, Miriam Larsson, Alexandre V Morozov, James R Broach, Stefan Björklund
Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin...
May 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28557307/pervasive-yet-nonuniform-contributions-of-dcp2-and-cnot7-to-maternal-mrna-clearance-in-zebrafish
#15
Yuichiro Mishima, Yukihide Tomari
mRNA degradation is a fundamental biological process that erases transcribed genetic information from cells. During maternal-to-zygotic transition of animal development, thousands of maternal mRNAs are degraded by multiple mechanisms including microRNAs and codon-mediated decay. Enzymatic requirements for maternal mRNA clearance, however, are not fully understood. Here, we analyzed a contribution of the decapping enzyme Dcp2 to maternal mRNA clearance in zebrafish by over-expressing catalytically inactive Dcp2 and performing RNA-seq analysis...
May 30, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28554132/the-human-rna-surveillance-factor-up-frameshift-1-inhibits-hepatic-cancer-progression-by-targeting-mrp2-abcc2
#16
Hai Zhang, Yina You, Zhongliang Zhu
Although the roles of Up-frameshift 1 (UPF1) in hepatocellular carcinoma (HCC) have been partly revealed, the detailed mechanisms remain poorly understood. Here, quantitative real-time PCR (qRT-PCR) and immunohistochemistry assays indicated that UPF1 expression was decreased in HCC tissues compared to the corresponding adjacent tissues, and was negatively correlated with MRP2/ABCC2 expression. Cell viability and apoptosis analyses showed that overexpression of UPF1 enhanced HCC cell sensitivity to sorafenib treatment, while knockdown of UPF1 decreased the sensitivity...
May 26, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28549954/amlexanox-enhances-premature-termination-codon-read-through-in-col7a1-and-expression-of-full-length-type-vii-collagen-potential-therapy-for-recessive-dystrophic-epidermolysis-bullosa
#17
Velina S Atanasova, Qiujie Jiang, Marco Prisco, Christina Gruber, Josefina Piñón Hofbauer, Mei Chen, Cristina Has, Leena Bruckner-Tuderman, John A McGrath, Jouni Uitto, Andrew P South
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare monogenic blistering disorder caused by lack of functional type VII collagen, leading to skin fragility and subsequent trauma-induced separation of the epidermis from the underlying dermis. 46% of RDEB patients harbor at least one premature termination codon (PTC) mutation in COL7A1 and previous studies have shown that aminoglycosides are able to overcome RDEB PTC mutations by inducing "read-through" and incorporation of an amino acid at the PTC site...
May 23, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28549443/quantitative-analysis-of-cryptic-splicing-associated-with-tdp-43-depletion
#18
Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M Isaacs, Vincent Plagnol
BACKGROUND: Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown...
May 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28545127/improvement-of-alt-decay-kinetics-by-all-oral-hcv-treatment-role-of-ns5a-inhibitors-and-differences-with-ifn-based-regimens
#19
Valeria Cento, Thi Huyen Tram Nguyen, Domenico Di Carlo, Elisa Biliotti, Laura Gianserra, Ilaria Lenci, Daniele Di Paolo, Vincenza Calvaruso, Elisabetta Teti, Maddalena Cerrone, Dante Romagnoli, Michela Melis, Elena Danieli, Barbara Menzaghi, Ennio Polilli, Massimo Siciliano, Laura Ambra Nicolini, Antonio Di Biagio, Carlo Federico Magni, Matteo Bolis, Francesco Paolo Antonucci, Velia Chiara Di Maio, Roberta Alfieri, Loredana Sarmati, Paolo Casalino, Sergio Bernardini, Valeria Micheli, Giuliano Rizzardini, Giustino Parruti, Tiziana Quirino, Massimo Puoti, Sergio Babudieri, Antonella D'Arminio Monforte, Massimo Andreoni, Antonio Craxì, Mario Angelico, Caterina Pasquazzi, Gloria Taliani, Jeremie Guedj, Carlo Federico Perno, Francesca Ceccherini-Silberstein
BACKGROUND: Intracellular HCV-RNA reduction is a proposed mechanism of action of direct-acting antivirals (DAAs), alternative to hepatocytes elimination by pegylated-interferon plus ribavirin (PR). We modeled ALT and HCV-RNA kinetics in cirrhotic patients treated with currently-used all-DAA combinations to evaluate their mode of action and cytotoxicity compared with telaprevir (TVR)+PR. STUDY DESIGN: Mathematical modeling of ALT and HCV-RNA kinetics was performed in 111 HCV-1 cirrhotic patients, 81 treated with all-DAA regimens and 30 with TVR+PR...
2017: PloS One
https://www.readbyqxmd.com/read/28542621/enzymatic-activity-necessary-to-restore-the-lethality-due-to-escherichia-coli-rnase-e-deficiency-is-distributed-among-bacteria-lacking-rnase-e-homologues
#20
Masaru Tamura, Daisuke Kageyama, Naoko Honda, Hirofumi Fujimoto, Atsushi Kato
Escherichia coli RNase E (Eco-RNase E), encoded by rne (Eco-rne), is considered the global RNA decay initiator. Although Eco-RNase E is an essential gene product in E. coli, some bacterial species, such as Bacillus subtilis, do not possess Eco-RNase E sequence homologues. B. subtilis instead possesses RNase J1/J2 (Bsu-RNase J1/J2) and RNase Y (Bsu-RNase Y) to execute RNA decay. Here we found that E. coli lacking the Eco-rne gene (Δrne E. coli) was viable conditional on M9 minimal media by introducing Bsu-RNase J1/J2 or Bsu-RNase Y...
2017: PloS One
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