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https://www.readbyqxmd.com/read/28813667/human-gw182-paralogs-are-the-central-organizers-for-rna-mediated-control-of-transcription
#1
Jessica A Hicks, Liande Li, Masayuki Matsui, Yongjun Chu, Oleg Volkov, Krystal C Johnson, David R Corey
In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles. Here, we reveal that the human GW182 paralogs TNRC6A/B/C are central organizing factors critical to RNA-mediated transcriptional activation. Mass spectrometry of purified nuclear lysates followed by experimental validation demonstrates that TNRC6A interacts with proteins involved in protein degradation, RNAi, the CCR4-NOT complex, the mediator complex, and histone-modifying complexes...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28813501/durum-wheat-mirnas-in-response-to-nitrogen-starvation-at-the-grain-filling-stage
#2
Diana L Zuluaga, Domenico De Paola, Michela Janni, Pasquale Luca Curci, Gabriella Sonnante
Durum wheat highly depends on nitrogen for seed development and yield, and the obtainment of varieties with a better nitrogen use efficiency is crucial to reduce production costs and environmental pollution. In this study, sequencing of two small RNA libraries obtained from tissues of Ciccio and Svevo cultivars grown under nitrogen starvation conditions produced 84 novel, and 161 conserved miRNAs. Of these, 7 novel and 13 known miRNAs were newly identified in this work. Quantitative PCR analysis of selected miRNAs highlighted that the expression levels of some of them depends on the tissue and on the cultivar, Svevo being the most responsive to nitrogen starvation...
2017: PloS One
https://www.readbyqxmd.com/read/28813447/the-use-of-high-throughput-small-rna-sequencing-reveals-differentially-expressed-micrornas-in-response-to-aster-yellows-phytoplasma-infection-in-vitis-vinifera-cv-chardonnay
#3
Marius C Snyman, Marie-Chrystine Solofoharivelo, Rose Souza-Richards, Dirk Stephan, Shane Murray, Johan T Burger
Phytoplasmas are cell wall-less plant pathogenic bacteria responsible for major crop losses throughout the world. In grapevine they cause grapevine yellows, a detrimental disease associated with a variety of symptoms. The high economic impact of this disease has sparked considerable interest among researchers to understand molecular mechanisms related to pathogenesis. Increasing evidence exist that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation during plant development and responses to biotic and abiotic stresses...
2017: PloS One
https://www.readbyqxmd.com/read/28811834/high-risk-human-papilloma-viruses-hpvs-are-present-in-benign-prostate-tissues-before-development-of-hpv-associated-prostate-cancer
#4
Wendy K Glenn, Christopher C Ngan, Timothy G Amos, Richard J Edwards, Joshua Swift, Louise Lutze-Mann, Fei Shang, Noel J Whitaker, James S Lawson
BACKGROUND: Although high risk HPVs are associated with an increased risk of prostate cancer it is not known if they have a causal role. The purpose of this study is to investigate the potential role of human papilloma viruses (HPVs) in prostate cancer. The aims are (i) to investigate the presence and confirm the identity of high risk HPVs in benign prostate tissues prior to the development of HPV positive prostate cancer in the same patients, and (ii) to determine if HPVs are biologically active...
2017: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/28811374/recruitment-of-crispr-cas-systems-by-tn7-like-transposons
#5
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28811264/protein-coding-genes-as-hosts-for-noncoding-rna-expression
#6
REVIEW
Vincent Boivin, Gabrielle Deschamps-Francoeur, Michelle S Scott
With the emergence of high-throughput sequence characterization methods and the subsequent improvements in gene annotations, it is becoming increasingly clear that a large proportion of eukaryotic protein-coding genes (as many as 50% in human) serve as host genes for non-coding RNA genes. Amongst the most extensively characterized embedded non-coding RNA genes, small nucleolar RNAs and microRNAs represent abundant families. Encoded individually or clustered, in sense or antisense orientation with respect to their host and independently expressed or dependent on host expression, the genomic characteristics of embedded genes determine their biogenesis and the extent of their relationship with their host gene...
August 12, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28810146/swarm-intelligence-enhanced-detection-of-non-small-cell-lung-cancer-using-tumor-educated-platelets
#7
Myron G Best, Nik Sol, Sjors G J G In 't Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N Niemeijer, Aniko V Fejes, Lee-Ann Tjon Kon Fat, Anna E Huis In 't Veld, Cyra Leurs, Tessa Y Le Large, Laura L Meijer, Irsan E Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward Post, Laurine E Wedekind, Jillian Bracht, Michelle Esenkbrink, Leon Wils, Francesca Favaro, Jilian D Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C de Jager, Rolf T Urbanus, Imo E Hoefer, Gerard Pasterkamp, Christine Mannhalter, Jose Gomez-Arroyo, Harm-Jan Bogaard, David P Noske, W Peter Vandertop, Daan van den Broek, Bauke Ylstra, R Jonas A Nilsson, Pieter Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent B Lewandrowski, Bakhos A Tannous, Adrianus J de Langen, Egbert F Smit, Michel M van den Heuvel, Thomas Wurdinger
Blood-based liquid biopsies, including tumor-educated blood platelets (TEPs), have emerged as promising biomarker sources for non-invasive detection of cancer. Here we demonstrate that particle-swarm optimization (PSO)-enhanced algorithms enable efficient selection of RNA biomarker panels from platelet RNA-sequencing libraries (n = 779). This resulted in accurate TEP-based detection of early- and late-stage non-small-cell lung cancer (n = 518 late-stage validation cohort, accuracy, 88%; AUC, 0.94; 95% CI, 0...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28808963/extraction-and-qpcr-based-detection-of-mirnas-from-cultured-pbmcs-of-bubaline-origin
#8
Chandra S Mukhopadhyay, Ramneek Verma, Jasdeep Singh
MicroRNAs are small noncoding but functionally important RNA molecules that are involved in regulating diverse cellular, metabolic, and immune processes. Their small size necessitates modification in traditional acid phenol-chloroform based RNA isolation procedures to get highly enriched fraction of small RNA that includes miRNAs and siRNAs . Further, of the different methods available, real-time PCR is a powerful tool for precise and specific detection and quantification of miRNA. Moreover, real-time PCR is used to validate the screening or expression of miRNAs that are discovered during high-throughput sequencing, or microarray analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808237/coding-and-small-non-coding-transcriptional-landscape-of-tuberous-sclerosis-complex-cortical-tubers-implications-for-pathophysiology-and-treatment
#9
James D Mills, Anand M Iyer, Jackelien van Scheppingen, Anika Bongaarts, Jasper J Anink, Bart Janssen, Till S Zimmer, Wim G Spliet, Peter C van Rijen, Floor E Jansen, Martha Feucht, Johannes A Hainfellner, Pavel Krsek, Josef Zamecnik, Katarzyna Kotulska, Sergiusz Jozwiak, Anna Jansen, Lieven Lagae, Paolo Curatolo, David J Kwiatkowski, R Jeroen Pasterkamp, Ketharini Senthilkumar, Lars von Oerthel, Marco F Hoekman, Jan A Gorter, Peter B Crino, Angelika Mühlebner, Brendon P Scicluna, Eleonora Aronica
Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808038/the-phosphatidylinositol-3-kinase-pathway-as-a-potential-therapeutic-target-in-bladder-cancer
#10
Shuxiong Zeng, Yanjun Zhu, Ai-Hong Ma, Weimin Yu, Hongyong Zhang, Tzu-Yin Lin, Wei Shi, Clifford G Tepper, Paul T Henderson, Susan Airhart, Jianming Guo, Chuanliang Xu, Ralph de Vere White, Chong-Xian Pan
PURPOSE: Activation of the phosphatidylinositol 3-kinase (PI3K) pathway occurs in over 40% of bladder urothelial cancers. The aim of this study is to determine the therapeutic potential, the underlying action and resistant mechanisms of drugs targeting the PI3K pathway. EXPERIMENTAL DESIGN: Urothelial cancer cell lines and patient-derived xenografts (PDXs) were analyzed for alterations of the PI3K pathway and for their sensitivity to the small molecule inhibitor pictilisib alone and in combination with cisplatin and/or gemcitabine...
August 14, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28805376/discovery-and-biosensing-applications-of-diverse-rna-cleaving-dnazymes
#11
Meng Liu, Dingran Chang, Yingfu Li
DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors...
August 14, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28803958/identification-and-characterization-of-lymph-organ-micrornas-in-red-swamp-crayfish-procambarus-clarkii-infected-with-white-spot-syndrome-virus
#12
Zhi-Qiang Du, Xiao-Yun Leng, Xiu-Li Shen, Yan-Hui Jin, Xin-Cang Li
MicroRNAs (miRNAs) were important post-transcriptional regulators and played vital roles in innate immunity system of invertebrates, especially in the aspect of antivirus. In this study, using high-throughput small RNAs Illumina sequencing system, differently expressed miRNAs (DEMs) from lymph organs in red swamp crayfish, Procambarus clarkii, infected with white spot syndrome virus, were identified. As a result, 32 known miRNAs and 7 novel miRNAs were identified in crayfish lymph organ small RNAs library of NG and WG...
August 10, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28803915/neural-crest-cell-implantation-restores-enteric-nervous-system-function-and-alters-the-gastrointestinal-transcriptome-in-human-tissue-engineered-small-intestine
#13
Christopher R Schlieve, Kathryn L Fowler, Matthew Thornton, Sha Huang, Ibrahim Hajjali, Xiaogang Hou, Brendan Grubbs, Jason R Spence, Tracy C Grikscheit
Acquired or congenital disruption in enteric nervous system (ENS) development or function can lead to significant mechanical dysmotility. ENS restoration through cellular transplantation may provide a cure for enteric neuropathies. We have previously generated human pluripotent stem cell (hPSC)-derived tissue-engineered small intestine (TESI) from human intestinal organoids (HIOs). However, HIO-TESI fails to develop an ENS. The purpose of our study is to restore ENS components derived exclusively from hPSCs in HIO-TESI...
August 9, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28803886/a-method-for-extracting-and-characterizing-rna-from-urine-for-downstream-pcr-and-rnaseq-analysis
#14
Kun Zhou, Monique A Spillman, Kian Behbakht, Julia M Komatsu, Juan E Abrahante, Douglas Hicks, Brent Schotl, Evan Odean, Kenneth L Jones, Michael W Graner, Lynne T Bemis
Readily accessible samples such as urine or blood are seemingly ideal for differentiating and stratifying patients; however, it has proven a daunting task to identify reliable biomarkers in such samples. Noncoding RNA holds great promise as a source of biomarkers distinguishing physiologic wellbeing or illness. Current methods to isolate and characterize RNA molecules in urine are limited. In this proof of concept study, we present a method to extract and identify small noncoding RNAs in urine. Initially, quantitative reverse transcription PCR was applied to confirm the presence of microRNAs in total RNA extracted from urine...
August 10, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28803540/preparation-of-highly-multiplexed-small-rna-sequencing-libraries
#15
Helena Persson, Rolf Søkilde, Anna Chiara Pirona, Carlos Rovira
MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples...
August 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28802831/validation-of-a-targeted-rna-sequencing-assay-for-kinase-fusion-detection-in-solid-tumors
#16
Julie W Reeser, Dorrelyn Martin, Jharna Miya, Esko A Kautto, Ezra Lyon, Eliot Zhu, Michele R Wing, Amy Smith, Matthew Reeder, Eric Samorodnitsky, Hannah Parks, Karan R Naik, Joseph Gozgit, Nicholas Nowacki, Kurtis D Davies, Marileila Varella-Garcia, Lianbo Yu, Aharon G Freud, Joshua Coleman, Dara L Aisner, Sameek Roychowdhury
Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior knowledge of fusion break points. To address this, we have analytically validated a targeted RNA sequencing assay (OSU-SpARKFuse) for fusion detection that interrogates complete transcripts from 93 kinase and transcription factor genes. From a total of 74 positive and 36 negative control samples, OSU-SpARKFuse had 93...
August 8, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28802262/small-noncoding-rna-expression-during-extreme-anoxia-tolerance-of-annual-killifish-austrofundulus-limnaeus-embryos
#17
Claire Louise Riggs, Jason E Podrabsky
Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance...
August 11, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28801656/comprehensive-mirna-expression-profiling-in-human-t-cell-acute-lymphoblastic-leukemia-by-small-rna-sequencing
#18
Annelynn Wallaert, Wouter Van Loocke, Lucie Hernandez, Tom Taghon, Frank Speleman, Pieter Van Vlierberghe
T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that can be classified into different molecular genetic subtypes according to their mRNA gene expression profile. In this study, we applied RNA sequencing to investigate the full spectrum of miRNA expression in primary T-ALL patient samples, T-ALL leukemia cell lines and healthy donor thymocytes. Notably, this analysis revealed that genetic subtypes of human T-ALL also display unique miRNA expression signatures, which are largely conserved in human T-ALL cell lines with corresponding genetic background...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801581/bpifcl-modulates-kiss2-expression-under-the-influence-of-11-ketotestosterone-in-female-zebrafish
#19
Shogo Moriya, Nabila Tahsin, Ishwar S Parhar
The bactericidal/permeability-increasing (BPI) fold-containing (BPIF) superfamily of genes expressed in the brain are purportedly involved in modulating brain function in response to stress, such as inflammation. Kisspeptin, encoded by kiss, is affected by inflammation in the brain; therefore, BPIF family genes might be involved in the modulation of kisspeptin in the brain. In this study, we investigated the expression of BPIF family C, like (bpifcl) in zebrafish brain and its involvement in kiss2 regulation...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800967/role-of-prion-protein-in-premature-senescence-of-human-fibroblasts
#20
Emmanuelle Boilan, Virginie Winant, Elise Dumortier, Benaissa ElMoualij, Pascale Quatresooz, Heinz D Osiewacz, Florence Debacq-Chainiaux, Olivier Toussaint
Prion protein (PrP) is essentially known for its capacity to induce neurodegenerative prion diseases in mammals caused by a conformational change in its normal cellular isoform (PrP(C)) into an infectious and disease-associated misfolded form, called scrapie isoform (PrP(Sc)). Although its sequence is highly conserved, less information is available on its physiological role under normal conditions. However, increasing evidence supports a role for PrP(C) in the cellular response to oxidative stress. In the present study, a new link between PrP and senescence is highlighted...
August 8, 2017: Mechanisms of Ageing and Development
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