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https://www.readbyqxmd.com/read/28077064/an-internet-based-bioinformatics-toolkit-for-plant-biosecurity-diagnosis-and-surveillance-of-viruses-and-viroids
#1
Roberto A Barrero, Kathryn R Napier, James Cunnington, Lia Liefting, Sandi Keenan, Rebekah A Frampton, Tamas Szabo, Simon Bulman, Adam Hunter, Lisa Ward, Mark Whattam, Matthew I Bellgard
BACKGROUND: Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways...
January 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28072746/znf148-modulates-top2a-expression-and-cell-proliferation-via-cerna-regulatory-mechanism-in-colorectal-cancer
#2
Xian Hua Gao, Juan Li, Yan Liu, Qi Zhi Liu, Li Qiang Hao, Lian Jie Liu, Wei Zhang
BACKGROUND: Competing endogenous RNA (ceRNA) regulation is a novel hypothesized mechanism that states RNA molecules share common target microRNAs (miRNAs) and may competitively combine into the same miRNA pool. METHODS: Zinc finger protein 148 (ZNF148) and TOP2A expression were analyzed in 742 colorectal cancer (CRC) tissues using immunohistochemistry (IHC). ZNF148 mRNA, TOP2A mRNA, miR101, miR144, miR335, and miR365 expression were estimated in 53 fresh frozen CRC tissues by reverse transcription polymerase chain reaction...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28069892/post-translational-regulation-of-the-dicing-activities-of-arabidopsis-dicer-like-3-and-4-by-inorganic-phosphate-and-the-redox-state
#3
Atsushi Seta, Midori Tabara, Yuki Nishibori, Akihiro Hiraguri, Naoko Ohkama-Ohtsu, Tadashi Yokoyama, Satoshi Hara, Keisuke Yoshida, Toru Hisabori, Akihito Fukudome, Hisashi Koiwa, Hiromitsu Moriyama, Nobuhiro Takahashi, Toshiyuki Fukuhara
In Arabidopsis thaliana, small interfering RNAs (siRNAs) generated by two Dicer isoforms, DCL3 and DCL4, function in distinct epigenetic processes, i.e., RNA-directed DNA methylation and post-transcriptional gene silencing, respectively. Plants often respond to their environment by producing a distinct set of small RNAs; however, the mechanism for controlling the production of different siRNAs from the same dsRNA substrate remains unclear. We established a simple biochemical method to visualize the dsRNA-cleaving activities of DCL3 and DCL4 in cell-free extracts prepared from Arabidopsis seedlings...
January 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28058810/prediction-of-effective-rna-interference-targets-and-pathway-related-genes-in-lepidopteran-insects-by-rna-sequencing-analysis
#4
Ruo-Bing Guan, Hai-Chao Li, Xue-Xia Miao
When using RNAi to study gene functions in Lepidoptera insects, we discovered that some genes could not be suppressed, instead, their expression levels could be up-regulated by dsRNA. To predict which genes could be easily silenced, we treated the Asian corn borer (Ostrinia furnacalis) with dsGFP and dsMLP. A transcriptome sequence analysis was conducted using the cDNAs 6 h after treatment with dsRNA. The results indicated that 160 genes were up-regulated and 44 genes were down-regulated by the two dsRNAs. Then, 50 co-up-regulated, 25 co-down-regulated and 43 unaffected genes were selected to determine their RNAi responses...
January 6, 2017: Insect Science
https://www.readbyqxmd.com/read/28057021/treatment-of-intermittent-hypoxia-increases-phosphorylated-tau-in-the-hippocampus-via-biological-processes-common-to-aging
#5
Sosuke Yagishita, Seiya Suzuki, Keisuke Yoshikawa, Keiko Iida, Ayako Hirata, Masahiko Suzuki, Akihiko Takashima, Kei Maruyama, Akira Hirasawa, Takeo Awaji
Sleep-disordered breathing produces cognitive impairments, and is possibly associated with Alzheimer disease (AD). Intermittent hypoxia treatment (IHT), an experimental model for sleep-disordered breathing, results in cognitive impairments in animals via unknown mechanisms. Here, we exposed mice to IHT protocols, and performed biochemical analyses and microarray analyses regarding their hippocampal samples. In particular, we performed gene ontology (GO)-based microarray analysis to elucidate effects of IHT on hippocampal functioning, which were compared with the effects of various previously-reported experimental conditions on that (ref...
January 5, 2017: Molecular Brain
https://www.readbyqxmd.com/read/28053190/phobf1-a-petunia-ocs-element-binding-factor-plays-an-important-role-in-antiviral-rna-silencing
#6
Daoyang Sun, Shaohua Li, Lixin Niu, Michael S Reid, Yanlong Zhang, Cai-Zhong Jiang
Virus-induced gene silencing (VIGS) is a common reverse genetics strategy for characterizing the function of genes in plants. The detailed mechanism governing RNA silencing efficiency triggered by viruses is largely unclear. Here, we reveal that a petunia (Petunia hybrida) ocs element binding factor, PhOBF1, one of the basic leucine zipper (bZIP) transcription factors, was up-regulated by Tobacco rattle virus (TRV) infection. Simultaneous silencing of PhOBF1 and a reporter gene, phytoene desaturase (PDS) or chalcone synthase (CHS), by TRV-based VIGS led to a failure of the development of leaf photobleaching or the white-corollas phenotype...
January 4, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28053119/short-intron-derived-ncrnas
#7
Florent Hubé, Damien Ulveling, Alain Sureau, Sabrina Forveille, Claire Francastel
Introns represent almost half of the human genome, although they are eliminated from transcripts through RNA splicing. Yet, different classes of non-canonical miRNAs have been proposed to originate directly from intron splicing. Here, we considered the alternative splicing of introns as an interesting source of miRNAs, compatible with a developmental switch. We report computational prediction of new Short Intron-Derived ncRNAs (SID), defined as precursors of smaller ncRNAs like miRNAs and snoRNAs produced directly by splicing, and tested their dependence on each key factor in canonical or alternative miRNAs biogenesis (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2)...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28011236/micrornas-in-thyroid-development-function-and-tumorigenesis
#8
Cesar Seigi Fuziwara, Edna Teruko Kimura
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that modulate the vast majority of cellular processes. During development, the correct timing and expression of miRNAs in the tissue differentiation is essential for organogenesis and functionality. In thyroid gland, DICER and miRNAs are necessary for accurately establishing thyroid follicles and hormone synthesis. Moreover, DICER1 mutations and miRNA deregulation observed in human goiter influence thyroid tumorigenesis. The thyroid malignant transformation by MAPK oncogenes is accompanied by global miRNA changes, with a marked reduction of "tumor-suppressor" miRNAs and activation of oncogenic miRNAs...
December 21, 2016: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28003477/argonaute-proteins-regulate-hiv-1-multiply-spliced-rna-and-viral-production-in-a-dicer-independent-manner
#9
Agathe Eckenfelder, Emmanuel Ségéral, Natalia Pinzón, Damien Ulveling, Céline Amadori, Marine Charpentier, Sabine Nidelet, Jean-Paul Concordet, Jean-François Zagury, Jean-Christophe Paillart, Clarisse Berlioz-Torrent, Hervé Seitz, Stéphane Emiliani, Sarah Gallois-Montbrun
Argonaute (Ago) proteins associate with microRNAs (miRNAs) to form the core of the RNA-induced silencing complex (RISC) that mediates post-transcriptional gene silencing of target mRNAs. As key players in anti-viral defense, Ago proteins are thought to have the ability to interact with human immunodeficiency virus type 1 (HIV-1) RNA. However, the role of this interaction in regulating HIV-1 replication has been debated. Here, we used high throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) to explore the interaction between Ago2 and HIV-1 RNA in infected cells...
December 20, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28003412/dicer-maintains-the-identity-and-function-of-proprioceptive-sensory-neurons
#10
Sean Michael O'Toole, Monica M Ferrer, Jennifer Mekonnen, Haihan Zhang, Yasuyuki Shima, David R Ladle, Sacha B Nelson
Neuronal cell identity is established during development and must be maintained throughout an animal's life (Fishell and Heintz 2013). Transcription factors critical for establishing neuronal identity can be required for maintaining it (Deneris and Hobert 2014). Post-transcriptional regulation also plays an important role in neuronal differentiation (Bian and Sun 2011), but its role in maintaining cell identity is less established. To better understand how post-transcriptional regulation might contribute to cell identity, we examined the proprioceptive neurons in the dorsal root ganglion (DRG), a highly specialized sensory neuron class, with well established properties that distinguish them from other neurons in the ganglion...
December 21, 2016: Journal of Neurophysiology
https://www.readbyqxmd.com/read/27986463/tamoxifen-differentially-regulates-mir-29b-1-and-mir-29a-expression-depending-on-endocrine-sensitivity-in-breast-cancer-cells
#11
Penn Muluhngwi, Abirami Krishna, Stephany L Vittitow, Joshua T Napier, Kirsten M Richardson, Mackenzie Ellis, Justin L Mott, Carolyn M Klinge
Endocrine-resistance develops in ∼40% of breast cancer patients after tamoxifen (TAM) therapy. Although microRNAs are dysregulated in breast cancer, their contribution to endocrine-resistance is not yet understood. Previous microarray analysis identified miR-29a and miR-29b-1 as repressed by TAM in MCF-7 endocrine-sensitive breast cancer cells but stimulated by TAM in LY2 endocrine-resistant breast cancer cells. Here we examined the mechanism for the differential regulation of these miRs by TAM in MCF-7 versus TAM-resistant LY2 and LCC9 breast cancer cells and the functional role of these microRNAs in these cells...
December 13, 2016: Cancer Letters
https://www.readbyqxmd.com/read/27982092/incomplete-drb4-dependence-of-the-dcl4-mediated-antiviral-defense
#12
Xiaofeng Zhang, Xiuchun Zhang, Kunxin Wu, Zhixin Liu, Dawei Li, Feng Qu
The double-stranded RNA-binding protein DRB4 of Arabidopsis was shown previously to contribute to the DICER-LIKE 4 (DCL4)-mediated biogenesis of viral small interfering RNAs (vsiRNAs) of 21 nucleotides (nt) in size. However, it is unclear whether all 21-nt vsiRNAs are dependent on this DRB4-DCL4 partnership. To resolve this question, we generated dcl2drb4 and dcl4drb4 double knockout mutants, and subjected them to infections with CPB-CC-PDS, a turnip crinkle virus mutant capable of inducing silencing of the PHYTOENE DESATURASE gene...
December 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27981621/targeting-%C3%AE-catenin-in-hepatocellular-cancers-induced-by-co-expression-of-mutant-%C3%AE-catenin-and-k-ras-in-mice
#13
Junyan Tao, Rong Zhang, Sucha Singh, Minakshi Poddar, Emily Xu, Michael Oertel, Xin Chen, Shanthi Ganesh, Marc Abrams, Satdarshan P Monga
Recently we have shown that co-expression of hMet and mutant-β-catenin using sleeping beauty transposon/transposase leads to HCC in mice that represents around 10% of human HCC. In the current study, we investigate if Ras activation, which can occur downstream of Met signaling, is sufficient to cause HCC in association with mutant-β-catenin. We also tested therapeutic efficacy of targeting β-catenin in HCC model. We show that mutant-K-Ras (G12D), which leads to Ras activation, cooperates with β-catenin mutants (S33Y, S45Y) to yield HCC in mice...
December 16, 2016: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/27980061/a-specific-dsrna-binding-protein-complex-selectively-sequesters-endogenous-inverted-repeat-sirna-precursors-and-inhibits-their-processing
#14
Thomas Montavon, Yerim Kwon, Aude Zimmermann, Philippe Hammann, Timothée Vincent, Valérie Cognat, Fabrice Michel, Patrice Dunoyer
In plants, several dsRNA-binding proteins (DRBs) have been shown to play important roles in various RNA silencing pathways, mostly by promoting the efficiency and/or accuracy of Dicer-like proteins (DCL)-mediated small RNA production. Among the DRBs encoded by the Arabidopsis genome, we recently identified DRB7.2 whose function in RNA silencing was unknown. Here, we show that DRB7.2 is specifically involved in siRNA production from endogenous inverted-repeat (endoIR) loci. This function requires its interacting partner DRB4, the main cofactor of DCL4 and is achieved through specific sequestration of endoIR dsRNA precursors, thereby repressing their access and processing by the siRNA-generating DCLs...
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27975100/hyperglycemia-suppresses-microrna-expression-in-platelets-to-increase-p2ry12-and-selp-levels-in-type-2-diabetes-mellitus
#15
Zsolt Fejes, Szilárd Póliska, Zsolt Czimmerer, Miklós Káplár, András Penyige, Gabriella Gál Szabó, Ildikó Beke Debreceni, Satya P Kunapuli, János Kappelmayer, Béla Nagy
Megakaryocyte (MK)-derived miRNAs have been detected in platelets. Here, we analysed the expression of platelet and circulating miR-223, miR-26b, miR-126 and miR-140 that might be altered with their target mRNAs in type 2 diabetes mellitus (DM2). MiRNAs were isolated from leukocyte-depleted platelets and plasma samples obtained from 28 obese DM2, 19 non-DM obese and 23 healthy individuals. The effect of hyperglycaemia on miRNAs was also evaluated in MKs using MEG-01 and K562 cells under hyperglycaemic conditions after 8 hours up to four weeks...
December 15, 2016: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/27959491/discovery-of-inhibitors-of-microrna-21-processing-using-small-molecule-microarrays
#16
Colleen M Connelly, Robert E Boer, Michelle H Moon, Peter Gareiss, John S Schneekloth
The identification of small molecules that bind to and perturb the function of microRNAs is an attractive approach for the treatment for microRNA-associated pathologies. However, there are only a few small molecules known to interact directly with microRNAs. Here, we report the use of a small molecule microarray (SMM) screening approach to identify low molecular weight compounds that directly bind to a pre-miR-21 hairpin. Compounds identified using this approach exhibit good affinity for the RNA (ranging from 0...
December 23, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/27958768/dicer-like-4-is-involved-in-restricting-the-systemic-movement-of-zucchini-yellow-mosaic-virus-in-nicotiana-benthamiana
#17
Teresa Cordero, Lidia Cerdán, Alberto Carbonell, Konstantina Katsarou, Kriton Kalantidis, José-Antonio Daròs
Zucchini yellow mosaic virus (ZYMV) induces serious diseases in cucurbits. To create a tool to screen for resistance genes, we cloned a wild ZYMV isolate and inserted the visual marker Rosea1 to obtain recombinant clone ZYMV-Ros1. While in some plant-virus combinations Rosea1 induces accumulation of anthocyanins in infected tissues, ZYMV-Ros1 infection of cucurbits did not lead to detectable anthocyanin accumulation. However, the recombinant virus did induce dark red pigmentation in infected tissues of the model plant Nicotiana benthamiana...
December 13, 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27956586/dna-methylation-influences-the-expression-of-dicer-like4-isoforms-which-encode-proteins-of-alternative-localization-and-function
#18
Nathan Pumplin, Alexis Sarazin, Pauline E Jullien, Nicolas G Bologna, Stefan Oberlin, Olivier Voinnet
Plant RNA silencing operates via RNA-directed DNA-methylation (RdDM) to repress transcription or by targeting mRNAs via posttranscriptional gene silencing (PTGS). These pathways rely on distinct Dicer-like (DCL) proteins that process double-stranded RNA (dsRNA) into small-interfering RNAs (siRNAs). Here, we explored the expression and subcellular localization of Arabidopsis thaliana DCL4. DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein, which also represents the ancestral form in plants...
November 2016: Plant Cell
https://www.readbyqxmd.com/read/27935420/the-epigenetic-regulation-of-dicer-and-microrna-biogenesis-by-panobinostat
#19
Nicholas C Hoffend, William J Magner, Thomas B Tomasi
microRNAs (miRs) are small noncoding RNAs that regulate/fine tune many cellular protein networks by targeting mRNAs for either degradation or translational inhibition. Dicer, a type III endoribonuclease, is a critical component in miR biogenesis and is required for mature mRNA production. Abnormal Dicer expression occurs in numerous cancer types and correlates with poor patient prognosis. Recent reports have demonstrated that epigenetic agents, including histone deacetylase inhibitors (HDACi), may regulate Dicer and miR expression...
December 9, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27934859/trbp-ensures-efficient-dicer-processing-of-precursor-microrna-in-rna-crowded-environments
#20
Mohamed Fareh, Kyu-Hyeon Yeom, Anna C Haagsma, Sweeny Chauhan, Inha Heo, Chirlmin Joo
The RNA-binding protein TRBP is a central component of the Dicer complex. Despite a decade of biochemical and structural studies, the essential functionality of TRBP in microRNA (miRNA) biogenesis remains unknown. Here we show that TRBP is an integral cofactor for time-efficient Dicer processing in RNA-crowded environments. We competed for Dicer processing of pre-miRNA with a large amount of cellular RNA species and found that Dicer-TRBP, but not Dicer alone, remains resilient. To apprehend the mechanism of this substrate selectivity, we use single-molecule fluorescence...
December 9, 2016: Nature Communications
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