keyword
MENU ▼
Read by QxMD icon Read
search

SRNA

keyword
https://www.readbyqxmd.com/read/28805544/rna-silencing-in-plant-symbiotic-bacteria-insights-from-a-protein-centric-view
#1
José I Jiménez-Zurdo, Marta Robledo
Extensive work in model enterobacteria has evidenced that the RNA chaperone Hfq and several endoribonucleases, such as RNase E or RNase III, serve pivotal roles in small RNA-mediated post-transcriptional silencing of gene expression. Characterization of these protein hubs commonly provide global functional and mechanistic insights into complex sRNA regulatory networks. The legume endosymbiont Sinorhizobium meliloti is a non-classical model bacterium with a very complex lifestyle in which riboregulation is expected to play important adaptive functions...
August 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28796489/rational-modular-rna-engineering-based-on-in-vivo-profiling-of-structural-accessibility
#2
Abigail N Leistra, Paul Amador, Aishwarya Buvanendiran, Alex Moon-Walker, Lydia M Contreras
Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering...
August 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28794186/hfq-links-translation-repression-to-stress-induced-mutagenesis-in-e-coli
#3
Jiandong Chen, Susan Gottesman
Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA-RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis...
August 9, 2017: Genes & Development
https://www.readbyqxmd.com/read/28763494/global-assessment-of-small-rnas-reveals-a-non-coding-transcript-involved-in-biofilm-formation-and-attachment-in-acinetobacter-baumannii-atcc-17978
#4
Laura Álvarez-Fraga, Soraya Rumbo-Feal, Astrid Pérez, Manuel J Gómez, Carmen Gayoso, Juan A Vallejo, Emily J Ohneck, Jaione Valle, Luis A Actis, Alejandro Beceiro, Germán Bou, Margarita Poza
Many strains of Acinetobacter baumannii have been described as being able to form biofilm. Small non-coding RNAs (sRNAs) control gene expression in many regulatory circuits in bacteria. The aim of the present work was to provide a global description of the sRNAs produced both by planktonic and biofilm-associated (sessile) cells of A. baumannii ATCC 17978, and to compare the corresponding gene expression profiles to identify sRNAs molecules associated to biofilm formation and virulence. sRNA was extracted from both planktonic and sessile cells and reverse transcribed...
2017: PloS One
https://www.readbyqxmd.com/read/28756649/rnomic-identification-and-evaluation-of-npctb_6715-a-non-protein-coding-rna-gene-as-a-potential-biomarker-for-the-detection-of-mycobacterium-tuberculosis
#5
Priyatharisni Kanniappan, Siti Aminah Ahmed, Ganeswrie Rajasekaram, Citartan Marimuthu, Ewe Seng Ch'ng, Li Pin Lee, Carsten A Raabe, Timofey S Rozhdestvensky, Thean Hock Tang
Technological advances in RNA biology greatly improved transcriptome profiling during the last two decades. Besides the discovery of many small RNAs (sRNA) that are involved in the physiological and pathophysiological regulation of various cellular circuits, it becomes evident that the corresponding RNA genes might also serve as potential biomarkers to monitor the progression of disease and treatment. sRNA gene candidate npcTB_6715 was previously identified via experimental RNomic (unpublished data), and we report its application as potential biomarker for the detection of Mycobacterium tuberculosis (MTB) in patient samples...
July 29, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28754632/small-rna-profiling-reveals-important-roles-for-mirnas-in-arabidopsis-response-to-bacillus-velezensis-fzb42
#6
Shanshan Xie, Haiyang Jiang, Zhilan Xu, Qianqian Xu, Beijiu Cheng
Bacillus velezensis FZB42 (previously classified as Bacillus amyloliquefaciens FZB42) has been confirmed to successfully colonize plant roots and enhance defense response against pathogen infection. This study indicated that FZB42 inoculation enhanced Arabidopsis defense response against Pseudomonas syringae DC3000 through inducing the expression of PR1, PDF1.2 and stomata closure. To further clarify the induced defense response at miRNA level, sRNA libraries from Arabidopsis roots inoculated with FZB42 and control were constructed and sequenced...
July 25, 2017: Gene
https://www.readbyqxmd.com/read/28743867/using-rna-sequencing-to-identify-putative-competing-endogenous-rnas-cernas-potentially-regulating-fat-metabolism-in-bovine-liver
#7
Ruobing Liang, Bo Han, Qian Li, Yuwei Yuan, Jianguo Li, Dongxiao Sun
RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28738828/unraveling-multifaceted-contributions-of-small-regulatory-rnas-to-photomorphogenic-development-in-arabidopsis
#8
Meng-Chun Lin, Huang-Lung Tsai, Sim-Lin Lim, Shih-Tong Jeng, Shu-Hsing Wu
BACKGROUND: Post-transcriptional control of gene expression mediated by small regulatory RNAs (sRNAs) is vital for growth and development of diverse organisms. The biogenesis of sRNAs is regulated by both positive and negative regulators known to regulate photomorphogenic development. Two microRNAs (miRNAs), miR157 and miR319, also regulate photomorphogenesis. However, genome-wide profiling of sRNAs and their regulation of target genes during photomorphogenesis has been missing. We provide a comprehensive view of sRNA-controlled gene expression in this developmental process...
July 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#9
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28731203/ptenp1-inhibits-the-growth-of-esophageal-squamous-cell-carcinoma-by-regulating-socs6-expression-and-correlates-with-disease-prognosis
#10
Tuotuo Gong, Shuyu Zheng, Shan Huang, Shenbo Fu, Xuanwei Zhang, Shupei Pan, Tian Yang, Yuchen Sun, Ya Wang, Beina Hui, Jia Guo, Xiaozhi Zhang
PTEN pseudogene (PTENP1) has a tumor suppressive role in multiple cancers. However, its involvement in esophageal squamous cell carcinoma (ESCC) remains largely unknown. In this study, we set out to identify the role of PTENP1 in the development of ESCC. Gene Expression Omnibus database was employed to investigate the expression of PTENP1 in ESCC. sRNA target Database(StarBase v2.0) was used to query the downstream of PTENP1. Next, both in vitro and in vivo experiments were employed to explore the function...
July 21, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28724941/novel-small-rna-spike-in-oligonucleotides-enable-absolute-normalization-of-small-rna-seq-data
#11
Stefan Lutzmayer, Balaji Enugutti, Michael D Nodine
Normalization of high-throughput small RNA sequencing (sRNA-Seq) data is required to compare sRNA levels across different samples. Commonly used relative normalization approaches can cause erroneous conclusions due to fluctuating small RNA populations between tissues. We developed a set of sRNA spike-in oligonucleotides (sRNA spike-ins) that enable absolute normalization of sRNA-Seq data across independent experiments, as well as the genome-wide estimation of sRNA:mRNA stoichiometries when used together with mRNA spike-in oligonucleotides...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720814/small-rna-mediated-repression-of-subtilisin-production-in-bacillus-licheniformis
#12
Robert Hertel, Sandra Meyerjürgens, Birgit Voigt, Heiko Liesegang, Sonja Volland
The species Bacillus licheniformis includes important strains that are used in industrial production processes. Currently the physiological model used to adapt these processes is based on the closely related model organism B. subtilis. In this study we found that both organisms reveal significant differences in the regulation of subtilisin, their main natural protease and a product of industrial fermentation processes. We identified and characterized a novel antisense sRNA AprAs, which represents an RNA based repressor of apr, the gene encoding for the industrial relevant subtilisin protease...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717590/construction-of-a-fur-null-mutant-and-rna-sequencing-provide-deeper-global-understanding-of-the-aliivibrio-salmonicida-fur-regulon
#13
Sunniva Katharina Thode, Cecilie Bækkedal, Jenny Johansson Söderberg, Erik Hjerde, Hilde Hansen, Peik Haugen
BACKGROUND: The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its target genes. Due to its importance in virulence, the Fur regulon is well studied for several model bacteria. In our previous work, we used computational predictions and microarray to gain insights into Fur-regulation in Aliivibrio salmonicida, and have identified a number of genes and operons that appear to be under direct control of Fur...
2017: PeerJ
https://www.readbyqxmd.com/read/28711666/micrornas-associated-with-drought-response-in-the-pulse-crop-common-bean-phaseolus-vulgaris-l
#14
Jing Wu, Lanfen Wang, Shumin Wang
Drought stress significantly reduces common bean yields. Recently, some drought-related miRNAs were found in various plants. However, reports of miRNAs involved in drought stress in common bean are limited. Here, we obtained four sRNA samples from drought-tolerant and -sensitive cultivars of common bean that experienced with or without drought treatment. A total of 49 novel miRNAs and 120 known miRNAs were detected. Under drought treatment, 9 and 7 known miRNAs were down and up-regulated, respectively, and 5 and 3 of the novel miRNAs were increased and decreased, respectively...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28710366/mirnas-in-the-alga-chlamydomonas-reinhardtii-are-not-phylogenetically-conserved-and-play-a-limited-role-in-responses-to-nutrient-deprivation
#15
Adam Voshall, Eun-Jeong Kim, Xinrong Ma, Tomohito Yamasaki, Etsuko N Moriyama, Heriberto Cerutti
The unicellular alga Chlamydomonas reinhardtii contains many types of small RNAs (sRNAs) but the biological role(s) of bona fide microRNAs (miRNAs) remains unclear. To address their possible function(s) in responses to nutrient availability, we examined miRNA expression in cells cultured under different trophic conditions (mixotrophic in the presence of acetate or photoautotrophic in the presence or absence of nitrogen). We also reanalyzed miRNA expression data in Chlamydomonas subject to sulfur or phosphate deprivation...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28709615/transcriptional-profiling-of-rickettsia-prowazekii-coding-and-non-coding-transcripts-during-in-vitro-host-pathogen-and-vector-pathogen-interactions
#16
Casey L C Schroeder, Hema P Narra, Abha Sahni, Kamil Khanipov, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Natural pathogen transmission of Rickettsia prowazekii, the etiologic agent of epidemic typhus, to humans is associated with arthropods, including human body lice, ticks, and ectoparasites of eastern flying squirrel. Recently, we have documented the presence of small RNAs in Rickettsia species and expression of R. prowazekii sRNAs during infection of cultured human microvascular endothelial cells (HMECs), which represent the primary target cells during human infections. Bacterial noncoding transcripts are now well established as critical post-transcriptional regulators of virulence and adaptation mechanisms in varying host environments...
June 29, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28705956/rapid-recovery-gene-downregulation-during-excess-light-stress-and-recovery-in-arabidopsis
#17
Peter Alexander Crisp, Diep Ganguly, Aaron B Smith, Kevin D Murray, Gonzalo M Estavillo, Iain R Searle, Ethan Ford, Ozren Bogdanović, Ryan Lister, Justin O Borevitz, Steven R Eichten, Barry J Pogson
Stress recovery may prove to be a promising approach to increase plant performance, and theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as three minutes. We demonstrate that 87% of the stress-upregulated mRNAs analysed exhibit very rapid recovery. For instance, HSP101 abundance declined two-fold every 5.1 minutes. We term this phenomenon Rapid Recovery Gene Downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting...
July 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28700949/two-sets-of-piwi-proteins-are-involved-in-distinct-srna-pathways-leading-to-elimination-of-germline-specific-dna
#18
Dominique I Furrer, Estienne C Swart, Matthias F Kraft, Pamela Y Sandoval, Mariusz Nowacki
Piwi proteins and piRNAs protect eukaryotic germlines against the spread of transposons. During development in the ciliate Paramecium, two Piwi-dependent sRNA classes are involved in the elimination of transposons and transposon-derived DNA: scan RNAs (scnRNAs), associated with Ptiwi01 and Ptiwi09, and iesRNAs, whose binding partners we now identify as Ptiwi10 and Ptiwi11. scnRNAs derive from the maternal genome and initiate DNA elimination during development, whereas iesRNAs continue DNA targeting until the removal process is complete...
July 11, 2017: Cell Reports
https://www.readbyqxmd.com/read/28699365/activating-the-chromatin-by-noncoding-rnas
#19
Nihay Laham-Karam, Pia Laitinen, Tiia A Turunen, Seppo Ylä-Herttuala
SIGNIFICANCE: The extent and breadth of transcription have recently been uncovered and this has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realized and to date it appears that ncRNAs may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and posttranscriptional regulation, including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding...
August 10, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28698160/investigating-the-regulatory-roles-of-the-micrornas-and-the-argonaute-1-enriched-small-rnas-in-plant-metabolism
#20
Jingping Qin, Zhonghai Tang, Xiaoxia Ma, Yijun Meng
The biological roles of small RNAs (sRNAs) in metabolic processes are emerging. However, a systemic study is needed to investigate the wide-spread involvement of the sRNAs in plant metabolism. By using the metabolism-related transcripts retrieved from the public database Plant Metabolic Network, and the publicly available sRNA high-throughput sequencing data, large-scale target identification was performed for microRNAs (miRNAs) and Argonaute 1 (AGO1)-enriched sRNAs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa)...
July 8, 2017: Gene
keyword
keyword
30226
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"