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RNA Biology

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https://www.readbyqxmd.com/read/30223713/evaluation-of-methodologies-for-microrna-biomarker-detection-by-next-generation-sequencing
#1
Anna M L Coenen-Stass, Iddo Magen, Tony Brooks, Iddo Z Ben-Dov, Linda Greensmith, Eran Hornstein, Pietro Fratta
In recent years, microRNAs (miRNAs) in tissues and biofluids have emerged as a new class of promising biomarkers for numerous diseases. Blood-based biomarkers are particularly desirable since serum or plasma is easily accessible and can be sampled repeatedly. To comprehensively explore the biomarker potential of miRNAs, sensitive, accurate and cost-efficient miRNA profiling techniques are required. Next generation sequencing (NGS) is emerging as the preferred method for miRNA profiling; offering high sensitivity, single-nucleotide resolution and the possibility to profile a considerable number of samples in parallel...
September 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/30176159/identification-of-host-rnas-that-interact-with-ebv-noncoding-rna-eber2
#2
Adalena V Nanni, Nara Lee
Epstein-Barr virus (EBV) expresses an abundant nuclear noncoding RNA called EBER2, which interacts with and acts as a guide RNA for the host transcription factor PAX5. This ribonucleoprotein complex localizes to the terminal repeat (TR) regions of the EBV genome via RNA-RNA interactions between EBER2 and nascent transcripts originating from these target sites. Given the fact that EBER2 base pairs with a viral RNA, we developed a protocol to identify EBER2-interacting RNAs in a transcriptome-wide manner. Our approach entails psoralen-mediated crosslinking, selection with antisense oligonucleotides targeting EBER2, and RNase V1 digestion coupled to next-generation sequencing...
September 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/30176151/domain-definition-and-interaction-mapping-for-the-endonuclease-complex-hnob1-hpno1
#3
Finaritra Raoelijaona, Stéphane Thore, Sébastien Fribourg
Ribosome biogenesis requires a variety of trans-acting factors in order to produce functional ribosomal subunits. In human cells, the complex formed by the proteins hNob1 and hPno1 is crucial to the site 3 cleavage occurring at the 3'-end of 18S pre-rRNA. However, the properties and activity of this complex are still poorly understood. We present here a detailed characterization of hNob1 organization and its interaction with hPno1. We redefine the boundaries of the endonuclease PIN domain present in hNob1 and we further delineate the precise interacting modules required for complex formation in hNob1 and hPno1...
September 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/30157725/bioinformatic-evidence-of-widespread-priming-in-type-i-and-ii-crispr-cas-systems
#4
Thomas J Nicholson, Simon A Jackson, Bradley I Croft, Raymond H J Staals, Peter C Fineran, Chris M Brown
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invading genetic elements, such as plasmids, bacteriophages and archaeal viruses. They consist of cas genes and CRISPR loci, which store genetic memories of previously encountered invaders as short sequences termed spacers. Spacers determine the specificity of CRISPR-Cas defence and immunity can be gained or updated by the addition of new spacers into CRISPR loci. There are two main routes to spacer acquisition, which are known as naïve and primed CRISPR adaptation...
September 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/30109815/pam-identification-by-crispr-cas-effector-complexes-diversified-mechanisms-and-structures
#5
Daniel Gleditzsch, Patrick Pausch, Hanna Müller-Esparza, Ahsen Özcan, Xiaohan Guo, Gert Bange, Lennart Randau
Adaptive immunity of prokaryotes is mediated by CRISPR-Cas systems that employ a large variety of Cas protein effectors to identify and destroy foreign genetic material. The different targeting mechanisms of Cas proteins rely on the proper protection of the host genome sequence while allowing for efficient detection of target sequences, termed protospacers. A short DNA sequence, the protospacer-adjacent motif (PAM), is frequently used to mark proper target sites. Cas proteins have evolved a multitude of PAM-interacting domains, which enables them to cope with viral anti-CRISPR measures that alter the sequence or accessibility of PAM elements...
September 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/30153081/cross-cleavage-activity-of-cas6b-in-crrna-processing-of-two-different-crispr-cas-systems-in-methanosarcina-mazei-g%C3%A3-1
#6
Lisa Nickel, Andrea Ulbricht, Omer S Alkhnbashi, Konrad U Förstner, Liam Cassidy, Katrin Weidenbach, Rolf Backofen, Ruth A Schmitz
The clustered regularly interspaced short palindromic repeat (CRISPR) system is a prokaryotic adaptive defense system against foreign nucleic acids. In the methanoarchaeon Methanosarcina mazei Gö1, two types of CRISPR-Cas systems are present (type I-B and type III-C). Both loci encode a Cas6 endonuclease, Cas6b-IB and Cas6b-IIIC, typically responsible for maturation of functional short CRISPR RNAs (crRNAs). To evaluate potential cross cleavage activity, we biochemically characterized both Cas6b proteins regarding their crRNA binding behavior and their ability to process pre-crRNA from the respective CRISPR array in vivo...
September 13, 2018: RNA Biology
https://www.readbyqxmd.com/read/30146918/optimizing-dna-transduction-by-selection-of-mutations-that-evade-bacterial-defense-systems
#7
Oren Auster, Rea Globus, Ido Yosef, Udi Qimron
We recently developed a platform where phage-transducing particles optimize DNA delivery to a wide range of hosts. Here, we use this platform to optimize DNA transduction into hosts that naturally restrict specific DNA sequences. We first show that a specific plasmid is restricted for transduction into a particular Salmonella strain. Using the platform, we select for a mutated plasmid that overcomes the restriction barrier. Insertion of the non-mutated sequence into a permissive plasmid restricts transduction...
September 13, 2018: RNA Biology
https://www.readbyqxmd.com/read/30146914/stable-maintenance-of-the-rudivirus-sirv3-in-a-carrier-state-in-sulfolobus-islandicus-despite-activation-of-the-crispr-cas-immune-response-by-a-second-virus-smv1
#8
Pavlos Papathanasiou, Susanne Erdmann, Carlos Leon-Sobrino, Kundan Sharma, Henning Urlaub, Roger A Garrett, Xu Peng
Carrier state viral infection constitutes an equilibrium state in which a limited fraction of a cellular population is infected while the remaining cells are transiently resistant to infection. This type of infection has been characterized for several bacteriophages but not, to date, for archaeal viruses. Here we demonstrate that the rudivirus SIRV3 can produce a host-dependent carrier state infection in the model crenarchaeon Sulfolobus. SIRV3 only infected a fraction of a Sulfolobus islandicus REY15A culture over several days during which host growth was unimpaired and no chromosomal DNA degradation was observed...
September 13, 2018: RNA Biology
https://www.readbyqxmd.com/read/30200840/characterization-of-cis-acting-elements-that-control-oscillating-alternative-splicing
#9
Gesine Goldammer, Alexander Neumann, Miriam Strauch, Michaela Müller-Mcnicoll, Florian Heyd, Marco Preußner
Alternative splicing (AS) in response to changing external conditions often requires alterations in the ability of sequence-specific RNA-binding proteins to bind to cis-acting sequences in their target pre-mRNA. While daily oscillations in AS events have been described in several organisms, cis-acting sequences that control time of the day-dependent AS remain largely elusive. Here we define cis-regulatory RNA elements that control body-temperature driven rhythmic AS using the mouse U2af26 gene as a model system...
September 10, 2018: RNA Biology
https://www.readbyqxmd.com/read/30200821/single-molecule-long-read-transcriptome-profiling-of-platysternon-megacephalum-mitochondrial-genome-with-gene-rearrangement-and-control-region-duplication
#10
Jianjun Liu, Hui Jiang, Jiawei Zan, Yuantian Bao, Jinxiu Dong, Lei Xiong, Liuwang Nie
Platysternon megacephalum is the sole living representative of the poorly studied turtle lineage Platysternidae. Their mitochondrial genome has been subject to gene rearrangement and control region duplication, resulting in a unique mitochondrial gene order in vertebrates. In this study, we sequenced the first full-length turtle (P. megacephalum) liver transcriptome using single-molecule real-time sequencing to study the transcriptional mechanisms of its mitochondrial genome. ND5 and ND6 anti-sense (ND6AS) forms a single transcript with the same expression in the human mitochondrial genome, but here we demonstrated differential expression of the rearranged ND5 and ND6AS genes in P...
September 10, 2018: RNA Biology
https://www.readbyqxmd.com/read/30146924/assessing-the-partners-of-the-rbp9-mrnp-complex-in-trypanosoma-cruzi-using-shotgun-proteomics-and-rna-seq
#11
Helisa Helena Wippel, Alexandre Haruo Inoue, Newton Medeiros Vidal, Jimena Ferreira da Costa, Bruna Hilzendeger Marcon, Bruno Accioly Alves Romagnoli, Marlon Dias Mariano Santos, Paulo Costa Carvalho, Samuel Goldenberg, Lysangela Ronalte Alves
Gene expression regulation in trypanosomes differs from other eukaryotes due to absence of transcriptional regulation for most of their genes. RNA-binding proteins (RBPs) associate with mRNAs and other regulatory proteins to form ribonucleoprotein complexes (mRNPs), which play a major role in post-transcriptional regulation. Here, we show that RBP9 is a cytoplasmic RBP in Trypanosoma cruzi with one RNA-recognition motif (RRM). The RBP9 sedimentation profile in a sucrose gradient indicated its presence in cytoplasmic translational complexes, suggesting its involvement in translation regulation...
September 10, 2018: RNA Biology
https://www.readbyqxmd.com/read/30146915/non-coding-transcript-variants-of-protein-coding-genes-what-are-they-good-for
#12
Sonam Dhamija, Manoj B Menon
The total number of protein-coding genes in the human genome is not significantly higher than those in much simpler eukaryotes, despite a general increase in genome size proportionate to the organismal complexity. The large non-coding transcriptome and extensive differential splicing, are increasingly being accepted as the factors contributing to the complex mammalian physiology and architecture. Recent studies reveal additional layers of functional complexity: some long non-coding RNAs have been re-defined as micropeptide or microprotein encoding transcripts, and in turn some protein-coding RNAs are bifunctional and display also non-coding functions...
September 10, 2018: RNA Biology
https://www.readbyqxmd.com/read/29995562/knockdown-of-lncrna-bdnf-as-suppresses-neuronal-cell-apoptosis-via-downregulating-mir-130b-5p-target-gene-prdm5-in-acute-spinal-cord-injury
#13
Huafeng Zhang, Dongzhe Li, Yi Zhang, Jianqiang Li, Shengli Ma, Jianwei Zhang, Yuanyuan Xiong, Wengang Wang, Ning Li, Lei Xia
OBJECTIVE: The present study was designed to investigate the molecular mechanism and biological roles of lncRNA brain-derived neurotrophic factor antisense (lncRNA BDNF-AS) in acute spinal cord injury (ASCI). METHODS: The rat model of ASCI and hypoxic cellular model were established to detect the expression of BDNF-AS, miR-130b-5p, PR (PRDI-BF1 and RIZ) domain protein 5 (PRDM5) and cleaved caspase 3 (c-caspase 3) using qRT-PCR and western blot. Basso, Beattie and Bresnahan (BBB) score was carried out to assess neurological function...
September 10, 2018: RNA Biology
https://www.readbyqxmd.com/read/30196756/predicting-microrna-disease-associations-using-bipartite-local-models-and-hubness-aware-regression
#14
Xing Chen, Jun-Yan Cheng, Jun Yin
The development and progression of numerous complex human diseases have been confirmed to be associated with microRNAs (miRNAs) by various experimental and clinical studies. Predicting potential miRNA-disease associations can help us understand the underlying molecular and cellular mechanisms of diseases and promote the development of disease treatment and diagnosis. Due to the high cost of conventional experimental verification, proposing a new computational method for miRNA-disease association prediction is an efficient and economical way...
September 8, 2018: RNA Biology
https://www.readbyqxmd.com/read/30176155/start-structure-assisted-rna-translation
#15
Gilbert Eriani, Franck Martin
Cap-dependent translation initiation begins by assembly of a pre-initiation ribosomal complex that scans the 5' Untranslated Region in order to localise the start codon. During this process, RNA secondary structures are melted by RNA helicases. Guenther et al reported that the yeast helicase Ded1, an orthologue of the mammalian DDX3 helicase, is responsible for this activity. When Ded1 is non-functional, RNA structures in the 5'UTR promote translation initiation on Alternative Translation Initiation Sites (ATIS) lead to uORF translation and consequently down-regulation of the main ORF...
September 3, 2018: RNA Biology
https://www.readbyqxmd.com/read/30176153/ddx39b-promotes-translation-through-regulation-of-pre-ribosomal-rna-levels
#16
Sharad Awasthi, Baskar Chakrapani, Arun Mahesh, Pavithra L Chavali, Sreenivas Chavali, Arunkumar Dhayalan
DDX39B, a DExD RNA helicase, is known to be involved in various cellular processes such as mRNA export, splicing and translation. Previous studies showed that the overexpression of DDX39B promotes the global translation but inhibits the mRNA export in a dominant negative manner. This presents a conundrum as to how DDX39B overexpression would increase the global translation if it inhibits the nuclear export of mRNAs. We resolve this by showing that DDX39B affects the levels of pre-ribosomal RNA by regulating its stability as well as synthesis...
September 3, 2018: RNA Biology
https://www.readbyqxmd.com/read/30175688/internal-rnas-overlapping-coding-sequences-can-drive-the-production-of-alternative-proteins-in-archaea
#17
Felipe Ten-Caten, Ricardo Z N Vêncio, Alan Péricles R Lorenzetti, Lívia Soares Zaramela, Ana Carolina Santana, Tie Koide
Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs)...
September 2, 2018: RNA Biology
https://www.readbyqxmd.com/read/30130453/crispr-visualizer-rapid-identification-and-visualization-of-crispr-loci-via-an-automated-high-throughput-processing-pipeline
#18
Matthew A Nethery, Rodolphe Barrangou
A CRISPR locus, defined by an array of repeat and spacer elements, constitutes a genetic record of the ceaseless battle between bacteria and viruses, showcasing the genomic integration of spacers acquired from invasive DNA. In particular, iterative spacer acquisitions represent unique evolutionary histories and are often useful for high-resolution bacterial genotyping, including comparative analysis of closely related organisms, clonal lineages, and clinical isolates. Current spacer visualization methods are typically tedious and can require manual data manipulation and curation, including spacer extraction at each CRISPR locus from genomes of interest...
August 21, 2018: RNA Biology
https://www.readbyqxmd.com/read/30081762/rna-melting-and-rna-chaperone-activities-of-plant-cold-shock-domain-proteins-are-not-correlated
#19
Nikolay Zlobin, Konstantin Evlakov, Olga Tikhonova, Aleksey Babakov, Vasiliy Taranov
Cold shock domain proteins (CSDPs) participate in plant development and resistance, but the underlying molecular mechanisms are poorly understood. In this study, we demonstrated that the CSDPs, including EsCSDP1, EsCSDP2, and EsCSDP3, from the extremophyte Eutrema salsugineum possess all basic properties of RNA chaperones. EsCSDP1-3 melt secondary structures in RNAs with various nucleotide sequences and exhibit RNA chaperone activity in vitro. EsCSDP1 and EsCSDP3 were shown to have higher RNA melting activity, whereasile EsCSDP2 had higher RNA chaperone activity...
August 21, 2018: RNA Biology
https://www.readbyqxmd.com/read/29966484/global-characterization-of-the-dicer-like-protein-drnb-roles-in-mirna-biogenesis-in-the-social-amoeba-dictyostelium-discoideum
#20
Zhen Liao, Jonas Kjellin, Marc P Hoeppner, Manfred Grabherr, Fredrik Söderbom
Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals...
August 21, 2018: RNA Biology
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