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small RNA sequencing

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https://www.readbyqxmd.com/read/29785964/mechanism-of-selective-recruitment-of-rna-polymerases-ii-and-iii-to-snrna-gene-promoters
#1
Oleksandr Dergai, Pascal Cousin, Jerome Gouge, Karishma Satia, Viviane Praz, Tracy Kuhlman, Philippe Lhôte, Alessandro Vannini, Nouria Hernandez
RNA polymerase II (Pol II) small nuclear RNA (snRNA) promoters and type 3 Pol III promoters have highly similar structures; both contain an interchangeable enhancer and "proximal sequence element" (PSE), which recruits the SNAP complex (SNAPc). The main distinguishing feature is the presence, in the type 3 promoters only, of a TATA box, which determines Pol III specificity. To understand the mechanism by which the absence or presence of a TATA box results in specific Pol recruitment, we examined how SNAPc and general transcription factors required for Pol II or Pol III transcription of SNAPc-dependent genes (i...
May 21, 2018: Genes & Development
https://www.readbyqxmd.com/read/29783940/small-rna-based-prediction-of-hybrid-performance-in-maize
#2
Felix Seifert, Alexander Thiemann, Tobias A Schrag, Dominika Rybka, Albrecht E Melchinger, Matthias Frisch, Stefan Scholten
BACKGROUND: Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783855/iec-specific-igf1-promotes-the-expansion-of-intestinal-stem-cells-during-epithelial-regeneration-and-functions-on-the-intestinal-immune-homeostasis
#3
Yu Zheng, Yongli Song, Qi Han, Wenjie Liu, Jiuzhi Xu, Zhengquan Yu, Ran Zhang, Ning Li
It is well known that insulin-like growth factor 1 (IGF1) acts as a trophic factor in small intestine under both physiological and pathophysiological conditions. However, it still lacks direct in vivo evidence of the functions of intestinal epithelial cells (IECs)-specific IGF1 under both normal and pathological conditions. Using IEC-specific IGF1-knockout (cKO) mice and Lgr5-eGFP-CreERT mice, we demonstrate that IEC-specific IGF1 can enhance nutrient uptake, reduce protein catabolism and energy consumption, and promotes the proliferation and expansion of intestinal epithelial cells, including ISCs and intestinal secretory cells...
May 21, 2018: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29782846/abnormal-small-intestinal-epithelial-microvilli-in-patients-with-crohn-s-disease
#4
Kelli L VanDussen, Aleksandar Stojmirović, Katherine Li, Ta-Chiang Liu, Patrick K Kimes, Brian D Muegge, Katherine F Simpson, Matthew A Ciorba, Jacqueline G Perrigoue, Joshua R Friedman, Jennifer E Towne, Richard D Head, Thaddeus S Stappenbeck
BACKGROUND & AIMS: Crohn's disease (CD) presents as chronic and often progressive intestinal inflammation, but the contributing pathogenic mechanisms are unclear. We aimed to identify alterations in intestinal cells that could contribute to the chronic and progressive course of CD. METHODS: We took an unbiased, system-wide approach, performing sequence analysis of RNA extracted from formalin-fixed, paraffin-embedded ileal tissue sections from patients with CD (n=36) and without CD (controls, n=32)...
May 18, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29782545/rosmarinic-acid-is-a-novel-inhibitor-for-hepatitis-b-virus-replication-targeting-viral-epsilon-rna-polymerase-interaction
#5
Yuta Tsukamoto, Sotaro Ikeda, Koji Uwai, Riho Taguchi, Kazuaki Chayama, Takemasa Sakaguchi, Ryo Narita, Wan-Ling Yao, Fumihiko Takeuchi, Yukie Otakaki, Koichi Watashi, Takaji Wakita, Hiroki Kato, Takashi Fujita
Current therapeutics for hepatitis B virus (HBV) patients such as nucleoside analogs (NAs) are effective; however, new antiviral drugs against HBV are still desired. Since the interaction between the epsilon (ε) sequence of HBV pregenomic RNA and viral polymerase (Pol) is a key step in the HBV replication cycle, we aimed to identify small compounds for its inhibition, and established a pull-down assay system for the detection of ε-RNA-binding-Pol. Screening showed that 5 out of 3,965 compounds inhibited ε-Pol binding, and we identified rosmarinic acid, which exhibited specificity, as a potential antiviral agent...
2018: PloS One
https://www.readbyqxmd.com/read/29781987/retrospective-microrna-sequencing-complementary-dna-library-preparation-protocol-using-formalin-fixed-paraffin-embedded-rna-specimens
#6
Olivier Loudig, Christina Liu, Thomas Rohan, Iddo Z Ben-Dov
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29779700/plasma-circulating-extracellular-rnas-in-left-ventricular-remodeling-post-myocardial-infarction
#7
Kirsty M Danielson, Ravi Shah, Ashish Yeri, Xiaojun Liu, Fernando Camacho Garcia, Michael Silverman, Kahraman Tanriverdi, Avash Das, Chunyang Xiao, Michael Jerosch-Herold, Bobak Heydari, Siddique Abbasi, Kendall Van Keuren-Jensen, Jane E Freedman, Yaoyu E Wang, Anthony Rosenzweig, Raymond Y Kwong, Saumya Das
Despite substantial declines in mortality following myocardial infarction (MI), subsequent left ventricular remodeling (LVRm) remains a significant long-term complication. Extracellular small non-coding RNAs (exRNAs) have been associated with cardiac inflammation and fibrosis and we hypothesized that they are associated with post-MI LVRm phenotypes. RNA sequencing of exRNAs was performed on plasma samples from patients with "beneficial" (decrease LVESVI ≥ 20%, n = 11) and "adverse" (increase LVESVI ≥ 15%, n = 11) LVRm...
May 17, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29779223/gene-editing-vectors-for-studying-nicotinic-acetylcholine-receptors-in-cholinergic-transmission
#8
Can Peng, Yijin Yan, Veronica J Kim, Staci E Engle, Jennifer N Berry, J Michael McIntosh, Rachael L Neve, Ryan M Drenan
Nicotinic acetylcholine receptors (nAChRs), prototype members of the cys-loop ligand gated ion channel family, are key mediators of cholinergic transmission in the central nervous system. Despite their importance, technical gaps exist in our ability to dissect the function of individual subunits in the brain. To overcome these barriers, we designed CRISPR/Cas9 small guide RNA sequences (sgRNAs) for production of loss-of-function alleles in mouse nAChR genes. These sgRNAs were validated in vitro via deep sequencing...
May 19, 2018: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#9
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29778390/next-generation-sequencing-reveals-differentially-expressed-small-noncoding-rnas-in-uterine-leiomyoma
#10
Tsai-Der Chuang, Yeming Xie, Wei Yan, Omid Khorram
OBJECTIVE: To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN: Laboratory-based investigation. SETTING: Academic center. PATIENT(S): Women undergoing hysterectomy for benign indications. INTERVENTION(S): Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR)...
May 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29777089/human-plasma-and-serum-extracellular-small-rna-reference-profiles-and-their-clinical-utility
#11
Klaas E A Max, Karl Bertram, Kemal Marc Akat, Kimberly A Bogardus, Jenny Li, Pavel Morozov, Iddo Z Ben-Dov, Xin Li, Zachary R Weiss, Azadeh Azizian, Anuoluwapo Sopeyin, Thomas G Diacovo, Catherine Adamidi, Zev Williams, Thomas Tuschl
Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using combinations of denaturants, reducing agents, proteolysis, and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and exDNA from the same biofluid sample...
May 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29775598/selective-cytotoxicity-of-the-nampt-inhibitor-fk866-toward-gastric-cancer-cells-with-markers-of-the-epithelial-mesenchymal-transition-due-to-loss-of-naprt
#12
Jooyoung Lee, Hyosil Kim, Jae Eun Lee, Su-Jin Shin, Sejin Oh, Sungjin Kwon, Hakhyun Kim, Yoon Young Choi, Michael A White, Soonmyung Paik, Jae-Ho Cheong, Hyun Seok Kim
BACKGROUND & AIMS: Markers of the epithelial-mesenchymal transition (EMT) in gastric tumor tissues are associated with poor outcomes of patients. We performed a screen to identify pharmacologic compounds that kill gastric cancer cells with EMT-associated gene expression patterns and investigate their mechanisms. METHODS: We identified 29 gastric cancer cell lines with gene expression signature previously associated with an EMT subtype, based on data from RNA sequence analyses, and confirmed their mesenchymal phenotypes of 7 lines (Hs746T, SNU1750, MKN1, SK4, SNU484, SNU668, and YCC11), based in invasive activity and protein markers...
May 15, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29774543/human-monocyte-transciptional-profiling-identifies-interleukin-18-receptor-accessory-protein-and-lactoferrin-as-novel-immune-targets-in-hypertension
#13
Matthew R Alexander, Allison E Norlander, Fernando Elijovich, Ravi V Atreya, Amadou Gaye, Juan S Gnecco, Cheryl L Laffer, Cristi L Galindo, Meena S Madhur
BACKGROUND AND PURPOSE: Monocytes play a critical role in hypertension. The purpose of our study was to use an unbiased approach to determine whether hypertensive individuals on conventional therapy exhibit an altered monocyte gene expression profile and to perform validation studies of select genes to identify novel therapeutic targets for hypertension. EXPERIMENTAL APPROACH: Next-generation RNA sequencing identified differentially expressed genes in a small discovery cohort of normotensive and hypertensive individuals...
May 18, 2018: British Journal of Pharmacology
https://www.readbyqxmd.com/read/29774288/molecular-analysis-of-giardia-duodenalis-isolates-from-symptomatic-and-asymptomatic-children-from-la-habana-cuba
#14
Luis Enrique Jerez Puebla, Fidel A Núñez, Lissette Pérez Santos, Lázara Rojas Rivero, Isabel Martínez Silva, Lucía Ayllón Valdés, Iraís Atencio Millán, Norbert Müller
Giardiasis is considered the most common intestinal parasitic disease in humans worldwide. In Cuba, this infection has particularly a strong clinical impact on the child population. Giardia duodenalis is a highly diverse protozoan, which comprises a complex of eight morphologically identical genetic assemblages, further divided into sub-assemblages. The present study used triose phosphate isomerase ( tpi ) and small-subunit ribosomal RNA (SSU rRNA) genes as genetic markers for the identification of G. duodenalis assemblages and sub-assemblages in correlation with clinical and epidemiological data in children attended at the Paediatric Hospital "William Soler" and at Pedro Kouri Institute, between 2015 and 2016...
August 2017: Parasite Epidemiology and Control
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#15
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29774043/integration-of-the-pokeweed-mirna-and-mrna-transcriptomes-reveals-targeting-of-jasmonic-acid-responsive-genes
#16
Kira C M Neller, Alexander Klenov, Juan C Guzman, Katalin A Hudak
The American pokeweed plant, Phytolacca americana , displays broad-spectrum resistance to plant viruses and is a heavy metal hyperaccumulator. However, little is known about the regulation of biotic and abiotic stress responses in this non-model plant. To investigate the control of miRNAs in gene expression, we sequenced the small RNA transcriptome of pokeweed treated with jasmonic acid (JA), a hormone that mediates pathogen defense and stress tolerance. We predicted 145 miRNAs responsive to JA, most of which were unique to pokeweed...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29773992/functional-analysis-of-rna-interference-related-soybean-pod-borer-lepidoptera-genes-based-on-transcriptome-sequences
#17
Fanli Meng, Mingyu Yang, Yang Li, Tianyu Li, Xinxin Liu, Guoyue Wang, Zhanchun Wang, Xianhao Jin, Wenbin Li
RNA interference (RNAi) is useful for controlling pests of agriculturally important crops. The soybean pod borer (SPB) is the most important soybean pest in Northeastern Asia. In an earlier study, we confirmed that the SPB could be controlled via transgenic plant-mediated RNAi. Here, the SPB transcriptome was sequenced to identify RNAi-related genes, and also to establish an RNAi-of-RNAi assay system for evaluating genes involved in the SPB systemic RNAi response. The core RNAi genes, as well as genes potentially involved in double-stranded RNA (dsRNA) uptake were identified based on SPB transcriptome sequences...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29772702/exploration-of-aba-responsive-mirnas-reveals-a-new-hormone-signaling-crosstalk-pathway-regulating-root-growth-of-populus-euphratica
#18
Conglong Lian, Kun Yao, Hui Duan, Qing Li, Chao Liu, Weilun Yin, Xinli Xia
Abscisic acid (ABA) plays an important role in the regulation of plant adaptation, seed germination, and root development in plants. However, the mechanism of ABA regulation of root development is still poorly understood, especially through the miRNA-mediated pathway . Here, small RNA (sRNA)-seq and degradome-seq were used to analyze the miRNAs' responsive to ABA in the stems and roots of P. euphratica , a model tree species for abiotic stress-resistance research. In total, 255 unique mature sequences, containing 154 known miRNAs and 101 novel miRNAs were identified, among which 33 miRNAs and 54 miRNAs were responsive to ABA in the roots and stems, respectively...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#19
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29769334/reovirus-nonstructural-protein-%C3%AF-ns-acts-as-an-rna-stability-factor-promoting-viral-genome-replication
#20
Paula F Zamora, Liya Hu, Jonathan J Knowlton, Roni M Lahr, Rodolfo A Moreno, Andrea J Berman, B V Venkataram Prasad, Terence S Dermody
Viral nonstructural proteins, which are not packaged into virions, are essential for replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. Reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, activities of σNS during individual steps of the reovirus replication cycle are poorly understood...
May 16, 2018: Journal of Virology
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