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https://www.readbyqxmd.com/read/29792949/srnaome-and-transcriptome-analysis-provide-insight-into-chilling-response-of-cowpea-pods
#1
Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu Gao
Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pod's nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29788132/freiburg-rna-tools-a-central-online-resource-for-rna-focused-research-and-teaching
#2
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen
The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29783940/small-rna-based-prediction-of-hybrid-performance-in-maize
#3
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/29780373/regulation-mechanism-mediated-by-trans-encoded-srna-nc117-in-short-chain-alcohols-tolerance-in-synechocystis-sp-pcc-6803
#4
Yanqi Bi, Guangsheng Pei, Tao Sun, Zixi Chen, Lei Chen, Weiwen Zhang
Microbial small RNAs (sRNAs) play essential roles against many stress conditions in cyanobacteria. However, little is known on their regulatory mechanisms on biofuels tolerance. In our previous sRNA analysis, a trans -encoded sRNA Nc117 was found involved in the tolerance to ethanol and 1-butanol in Synechocystis sp. PCC 6803. However, its functional mechanism is yet to be determined. In this study, functional characterization of sRNA Nc117 was performed. Briefly, the exact length of the trans -encoded sRNA Nc117 was determined to be 102 nucleotides using 3' RACE, and the positive regulation of Nc117 on short chain alcohols tolerance was further confirmed...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773668/plants-send-small-rnas-in-extracellular-vesicles-to-fungal-pathogen-to-silence-virulence-genes
#5
Qiang Cai, Lulu Qiao, Ming Wang, Baoye He, Feng-Mao Lin, Jared Palmquist, Hsien-Da Huang, Hailing Jin
Some pathogens and pests deliver small RNAs (sRNAs) into host cells to suppress host immunity. Conversely, hosts also transfer sRNAs into pathogens and pests to inhibit their virulence. Although sRNA trafficking has been observed in a wide variety of interactions, how sRNAs are transferred, especially from hosts to pathogens/pests, is still unknown. Here we show that host Arabidopsis cells secrete exosome-like extracellular vesicles to deliver sRNAs into fungal pathogen Botrytis cinerea These sRNA-containing vesicles accumulate at the infection sites and are taken up by the fungal cells...
May 17, 2018: Science
https://www.readbyqxmd.com/read/29772702/exploration-of-aba-responsive-mirnas-reveals-a-new-hormone-signaling-crosstalk-pathway-regulating-root-growth-of-populus-euphratica
#6
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
#7
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/29769402/gtsf-1-is-required-for-formation-of-a-functional-rna-dependent-rna-polymerase-complex-in-caenorhabditis-elegans
#8
Miguel Vasconcelos Almeida, Sabrina Dietz, Stefan Redl, Emil Karaulanov, Andrea Hildebrandt, Christian Renz, Helle D Ulrich, Julian König, Falk Butter, René F Ketting
Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing...
May 16, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29762500/circulating-micrornas-in-young-patients-with-acute-coronary-syndrome
#9
Kind-Leng Tong, Ahmad Syadi Mahmood Zuhdi, Wan Azman Wan Ahmad, Paul M Vanhoutte, Joao Pedro de Magalhaes, Mohd Rais Mustafa, Pooi-Fong Wong
Circulating microRNAs (miRNAs) hold great potential as novel diagnostic markers for acute coronary syndrome (ACS). This study sought to identify plasma miRNAs that are differentially expressed in young ACS patients (mean age of 38.5 ± 4.3 years) and evaluate their diagnostic potentials. Small RNA sequencing (sRNA-seq) was used to profile plasma miRNAs. Discriminatory power of the miRNAs was determined using receiver operating characteristic (ROC) analysis. Thirteen up-regulated and 16 down-regulated miRNAs were identified in young ACS patients...
May 15, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29759067/small-rna-profiling-of-low-biomass-samples-identification-and-removal-of-contaminants
#10
Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, Joëlle V Fritz, Patrick May, Carine de Beaufort, Bimal B Upadhyaya, Anubrata Ghosal, David J Galas, Paul Wilmes
BACKGROUND: Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. DNA contamination has been previously reported, yet contamination with RNA is usually considered to be very unlikely due to its inherent instability. Small RNAs (sRNAs) identified in tissues and bodily fluids, such as blood plasma, have implications for physiology and pathology, and therefore the potential to act as disease biomarkers...
May 14, 2018: BMC Biology
https://www.readbyqxmd.com/read/29757397/uncovering-key-small-rnas-associated-with-gametocidal-action-in-wheat
#11
Dan Wang, Lei Ling, Wenrui Zhang, Yan Bai, Yongjun Shu, Changhong Guo
Gametocidal (Gc) chromosomes can kill gametes that lack them by causing chromosomal breakage to ensure their preferential transmission, and have been exploited in genetic breeding. The present study investigated the possible roles of small RNAs (sRNA) in Gc action. By sequencing two small RNA libraries from the anthers of Triticum aestivum cv. Chinese Spring (CS) and Chinese Spring-Gc 3C chromosome monosomic addition line (CS-3C), we identified 239 conserved and 72 putative novel microRNAs (miRNAs), including 135 differentially expressed miRNAs...
May 11, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29740417/the-small-regulatory-antisense-rna-pilr-affects-pilus-formation-and-cell-motility-by-negatively-regulating-pila11-in-synechocystis-sp-pcc-6803
#12
Jinlu Hu, Jiao Zhan, Hui Chen, Chenliu He, Huaixing Cang, Qiang Wang
Pili are found on the surface of many bacteria and play important roles in cell motility, pathogenesis, biofilm formation, and sensing and reacting to environmental changes. Cell motility in the model cyanobacterium Synechocystis sp. PCC 6803 relies on expression of the putative pilA9-pilA10-pilA11-slr2018 operon. In this study, we identified the antisense RNA PilR encoded in the noncoding strand of the prepilin-encoding gene pilA11 . Analysis of overexpressor [PilR(+)] and suppressor [PilR(-)] mutant strains revealed that PilR is a direct negative regulator of PilA11 protein...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29740411/an-srna-and-cold-shock-protein-homolog-based-feedforward-loop-post-transcriptionally-controls-cell-cycle-master-regulator-ctra
#13
Marta Robledo, Jan-Philip Schlüter, Lars O Loehr, Uwe Linne, Stefan P Albaum, José I Jiménez-Zurdo, Anke Becker
Adjustment of cell cycle progression is crucial for bacterial survival and adaptation under adverse conditions. However, the understanding of modulation of cell cycle control in response to environmental changes is rather incomplete. In α-proteobacteria, the broadly conserved cell cycle master regulator CtrA underlies multiple levels of control, including coupling of cell cycle and cell differentiation. CtrA levels are known to be tightly controlled through diverse transcriptional and post-translational mechanisms...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29733627/engineering-a-functional-small-rna-negative-autoregulation-network-with-model-guided-design
#14
Chelsea Yongxi Hu, Melissa K Takahashi, Yan Zhang, Julius B Lucks
RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal noise. Here we use cell-free transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR constructs...
May 7, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29730297/biological-and-regulatory-roles-of-acid-induced-small-rna-ryec-in-salmonella-typhimurium
#15
Daniel Ryan, Mohana Mukherjee, Ritu Nayak, Ria Dutta, Mrutyunjay Suar
Salmonella Typhimurium is an enteric pathogen that has evolved masterful strategies to enable survival under stress conditions both within and outside a host. The acid tolerance response (ATR) is one such mechanism that enhances the viability of acid adapted bacteria to lethal pH levels. While numerous studies exist on the protein coding components of this response, there is very little data on the roles of small RNAs (sRNAs). These non-coding RNA molecules have recently been shown to play roles as regulators of bacterial stress response and virulence pathways...
May 3, 2018: Biochimie
https://www.readbyqxmd.com/read/29730207/sports1-0-a-tool-for-annotating-and-profiling-non-coding-rnas-optimized-for-rrna-and-trna-derived-small-rnas
#16
Junchao Shi, Eun-A Ko, Kenton M Sanders, Qi Chen, Tong Zhou
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1...
May 3, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29728392/small-low-but-potent-the-complex-regulatory-role-of-the-small-rna-solb-on-solventogenesis-in-clostridium-acetobutylicum
#17
Alexander J Jones, Alan G Fast, Michael Clupper, Eleftherios T Papoutsakis
The recently revived Clostridium acetobutylicum based Acetone-Butanol-Ethanol (ABE) fermentation is widely celebrated and studied for its impact on industrial biotechnology. C. acetobutylicum has been extensively studied and engineered, yet critical areas of the molecular basis of how solvent formation is regulated remain unresolved. The core solventogenic genes ( adhE1/aad , ctfA , ctfB , adc ) are coded on the sol locus of the pSOL1 megaplasmid, whose loss leads to asporogenous, "degenerate" cells...
May 4, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29722807/the-uea-srna-workbench-version-4-4-a-comprehensive-suite-of-tools-for-analyzing-mirnas-and-srnas
#18
Matthew B Stocks, Irina Mohorianu, Matthew Beckers, Claudia Paicu, Simon Moxon, Joshua Thody, Tamas Dalmay, Vincent Moulton
Motivation: RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs. Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential...
May 2, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29719549/glassgo-automated-and-reliable-detection-of-srna-homologs-from-a-single-input-sequence
#19
Steffen C Lott, Richard A Schäfer, Martin Mann, Rolf Backofen, Wolfgang R Hess, Björn Voß, Jens Georg
Bacterial small RNAs (sRNAs) are important post-transcriptional regulators of gene expression. The functional and evolutionary characterization of sRNAs requires the identification of homologs, which is frequently challenging due to their heterogeneity, short length and partly, little sequence conservation. We developed the GLobal Automatic Small RNA Search go (GLASSgo) algorithm to identify sRNA homologs in complex genomic databases starting from a single sequence. GLASSgo combines an iterative BLAST strategy with pairwise identity filtering and a graph-based clustering method that utilizes RNA secondary structure information...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29718424/psrnatarget-a-plant-small-rna-target-analysis-server-2017-release
#20
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao
Plant regulatory small RNAs (sRNAs), which include most microRNAs (miRNAs) and a subset of small interfering RNAs (siRNAs), such as the phased siRNAs (phasiRNAs), play important roles in regulating gene expression. Although generated from genetically distinct biogenesis pathways, these regulatory sRNAs share the same mechanisms for post-translational gene silencing and translational inhibition. psRNATarget was developed to identify plant sRNA targets by (i) analyzing complementary matching between the sRNA sequence and target mRNA sequence using a predefined scoring schema and (ii) by evaluating target site accessibility...
April 30, 2018: Nucleic Acids Research
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