Evaluation of Alignment Algorithms for Discovery and Identification of Pathogens Using RNA-Seq. Next-generation sequencing technologies provide an unparallelled opportunity for the characterization and discovery of known and novel viruses. Because viruses are known to have the highest mutation rates when compared to eukaryotic and bacterial organisms, we assess the extent to which eleven well-known alignment algorithms (BLAST, BLAT, BWA, BWA-SW, BWA-MEM, BFAST, Bowtie2, Novoalign, GSNAP, SHRiMP2 and STAR) can be used for characterizing mutated and non-mutated viral sequences - including those that exhibit RNA splicing - in transcriptome samples. To evaluate aligners objectively we developed a realistic RNA-Seq simulation and evaluation framework (RiSER) and propose a new combined score to rank aligners for viral characterization in terms of their precision, sensitivity and alignment accuracy.
We used RiSER to simulate both human and viral read sequences and suggest the best set of aligners for viral sequence characterization in human transcriptome samples. Figures Editor: I. ). The Essential Role for the RNA Triphosphatase Cet1p in Nuclear Import of the mRNA Capping Enzyme Cet1p-Ceg1p Complex of Saccharomyces cerevisiae. mRNA capping is the first cotranscriptional modification of mRNA in the nucleus. In Saccharomyces cerevisiae, the first two steps of mRNA capping are catalyzed by the RNA triphosphatase Cet1p and the RNA guanylyltransferase Ceg1p. Cet1p and Ceg1p interact to form a mRNA capping enzyme complex and the guanylyltransferase activity of Ceg1p is stimulated by binding with Cet1p. The Cet1p-Ceg1p complex needs to be transported into the nucleus, where mRNA capping occurs. However, the molecular mechanism of nuclear transport of the Cet1p-Ceg1p complex is not known. Here, we show that Cet1p is responsible and that the Cet1p-Ceg1p interaction is essential for the nuclear localization of the Cet1p-Ceg1p complex.
Figures Citation: Takizawa N, Fujiwara T, Yamasaki M, Saito A, Fukao A, et al. (2013) The Essential Role for the RNA Triphosphatase Cet1p in Nuclear Import of the mRNA Capping Enzyme Cet1p-Ceg1p Complex of Saccharomyces cerevisiae. Editor: Akio Kanai, Keio University, Japan Introduction. Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets. Single-nucleotide polymorphisms (SNPs) contribute to the between-individual expression variation of many genes. A regulatory (trait-associated) SNP is usually located near or within a (host) gene, possibly influencing the gene’s transcription or/and post-transcriptional modification.
But its targets may also include genes that are physically farther away from it. A heuristic explanation of such multiple-target interferences is that the host gene transfers the SNP genotypic effects to the distant gene(s) by a transcriptional or signaling cascade. These connections between the host genes (regulators) and the distant genes (targets) make the genetic analysis of gene expression traits a promising approach for identifying unknown regulatory relationships. Figures Citation: Zhang W, Edwards A, Flemington EK, Zhang K (2013) Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets. Results. RNA-Sequencing Analysis of TCDD-Induced Responses in Zebrafish Liver Reveals High Relatedness to In Vivo Mammalian Models and Conserved Biological Pathways. Citation: Li Z-H, Xu H, Zheng W, Lam SH, Gong Z (2013) RNA-Sequencing Analysis of TCDD-Induced Responses in Zebrafish Liver Reveals High Relatedness to In Vivo Mammalian Models and Conserved Biological Pathways.
PLoS ONE 8(10): e77292. doi:10.1371/journal.pone.0077292 Editor: Zhanjiang Liu, Auburn University, United States of America Received: June 6, 2013; Accepted: September 1, 2013; Published: October 30, 2013 This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Funding: This work was supported by the Singapore National Research Foundation under its Environmental & Water Technologies Strategic Research Programme and administered by the Environment & Water Industry Programme Office (EWI) of the PUB (grant number R-154-000-328-272). Introduction Materials and Methods Zebrafish. EBUS-TBNA Provides Highest RNA Yield for Multiple Biomarker Testing from Routinely Obtained Small Biopsies in Non-Small Cell Lung Cancer Patients - A Comparative Study of Three Different Minimal Invasive Sampling Methods.
Background Multiple biomarker testing is necessary to facilitate individualized treatment of lung cancer patients. More than 80% of lung cancers are diagnosed based on very small tumor samples. Often there is not enough tissue for molecular analysis. We compared three minimal invasive sampling methods with respect to RNA quantity for molecular testing. Methods 106 small biopsies were prospectively collected by three different methods forceps biopsy, endobronchial ultrasound (EBUS) guided transbronchial needle aspiration (TBNA), and CT-guided core biopsy.
Samples were split into two halves. Results Overall, RNA-extraction was possible in 101 out of 106 patients (95.3%). Conclusion All three methods can provide sufficient tumor material for multiple biomarkers testing from routinely obtained small biopsies in lung cancer patients. Figures Editor: John D. Received: May 13, 2013; Accepted: September 6, 2013; Published: October 29, 2013 Copyright: © 2013 Schmid-Bindert et al. Introduction Patients. RNA-CODE: A Noncoding RNA Classification Tool for Short Reads in NGS Data Lacking Reference Genomes. The number of transcriptomic sequencing projects of various non-model organisms is still accumulating rapidly. As non-coding RNAs (ncRNAs) are highly abundant in living organism and play important roles in many biological processes, identifying fragmentary members of ncRNAs in small RNA-seq data is an important step in post-NGS analysis. However, the state-of-the-art ncRNA search tools are not optimized for next-generation sequencing (NGS) data, especially for very short reads.
In this work, we propose and implement a comprehensive ncRNA classification tool (RNA-CODE) for very short reads. RNA-CODE is specifically designed for ncRNA identification in NGS data that lack quality reference genomes. Given a set of short reads, our tool classifies the reads into different types of ncRNA families. The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively. Figures bases. Role of MicroRNA 1207-5P and Its Host Gene, the Long Non-Coding RNA Pvt1, as Mediators of Extracellular Matrix Accumulation in the Kidney: Implications for Diabetic Nephropathy.
Diabetic nephropathy is the most common cause of chronic kidney failure and end-stage renal disease in the Western World. One of the major characteristics of this disease is the excessive accumulation of extracellular matrix (ECM) in the kidney glomeruli. While both environmental and genetic determinants are recognized for their role in the development of diabetic nephropathy, epigenetic factors, such as DNA methylation, long non-coding RNAs, and microRNAs, have also recently been found to underlie some of the biological mechanisms, including ECM accumulation, leading to the disease. We previously found that a long non-coding RNA, the plasmacytoma variant translocation 1 (PVT1), increases plasminogen activator inhibitor 1 (PAI-1) and transforming growth factor beta 1 (TGF-β1) in mesangial cells, the two main contributors to ECM accumulation in the glomeruli under hyperglycemic conditions, as well as fibronectin 1 (FN1), a major ECM component.
Figures Editor: Leo TO. Introduction Results. Possible Formation of Mitochondrial-RNA Containing Chimeric or Trimeric RNA Implies a Post-Transcriptional and Post-Splicing Mechanism for RNA Fusion. Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs.
We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. Figures Citation: Yang W, Wu J-m, Bi A-d, Ou-yang Y-c, Shen H-h, et al. (2013) Possible Formation of Mitochondrial-RNA Containing Chimeric or Trimeric RNA Implies a Post-Transcriptional and Post-Splicing Mechanism for RNA Fusion. Editor: Arun Rishi, Wayne State University, United States of America Results. Scleral Micro-RNA Signatures in Adult and Fetal Eyes. Introduction In human eyes, ocular enlargement/growth reflects active extracellular matrix remodeling of the outer scleral shell. Micro-RNAs are small non-coding RNAs that regulate gene expression by base pairing with target sequences.
They serve as nodes of signaling networks. We hypothesized that the sclera, like most tissues, expresses micro-RNAs, some of which modulate genes regulating ocular growth. In this study, the scleral micro-RNA expression profile of rapidly growing human fetal eyes was compared with that of stable adult donor eyes using high-throughput microarray and quantitative PCR analyses. Methods Scleral samples from normal human fetal (24 wk) and normal adult donor eyes were obtained (n=4 to 6, each group), and RNA extracted.
Results Human sclera was found to express micro-RNAs, and comparison of microarray results for adult and fetal samples revealed many to be differentially expressed (p<0.01, min p= 6.5x1011). Conclusion Figures Copyright: © 2013 Metlapally et al. Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz. Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased.
Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC) Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a ‘stepwise ansatz’, recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. Figures Citation: Das R (2013) Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz. Introduction. Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs. Introduction Phytophthora species are a diverse group of filamentous, eukaryotic plant pathogens that are related to other stramenopile (heterokont) eukaryotes within the chromalveolate super-group [1], [2].
The stramenopile group includes golden-brown algae, diatoms, brown algae, and oomycetes. These diverse organisms, ranging from autotrophic algae to pathogenic, fungus-like oomycetes, were only recently grouped together based on phylogenetic analysis [1]. The oomycete lineage (non-photosynthetic stramenopiles, including the genus Phytophthora) was shown to be evolutionarily ancient. Eukaryotes use RNA-based pathways to regulate gene expression at the transcriptional and post-transcriptional levels.
In plants and animals, and several other eukaryotic lineages, microRNAs are ~20-24-nucleotide RNAs that mediate silencing of target transcripts post-transcriptionally. Another diverse class of small RNAs, referred to broadly as siRNA, are common to animals, plants, and fungi [18], [19]. A Core MRB1 Complex Component Is Indispensable for RNA Editing in Insect and Human Infective Stages of Trypanosoma brucei. The Conserved C-Terminus of the PcrA/UvrD Helicase Interacts Directly with RNA Polymerase. UvrD-like helicases play diverse roles in DNA replication, repair and recombination pathways.
An emerging body of evidence suggests that their different cellular functions are directed by interactions with partner proteins that target unwinding activity to appropriate substrates. Recent studies in E. coli have shown that UvrD can act as an accessory replicative helicase that resolves conflicts between the replisome and transcription complexes, but the mechanism is not understood. Here we show that the UvrD homologue PcrA interacts physically with B. subtilis RNA polymerase, and that an equivalent interaction is conserved in E. coli where UvrD, but not the closely related helicase Rep, also interacts with RNA polymerase.
The PcrA-RNAP interaction is direct and independent of nucleic acids or additional mediator proteins. Figures Editor: Maria Spies, University of Iowa, United States of America Received: July 11, 2013; Accepted: September 13, 2013; Published: October 16, 2013 Introduction. F11R Expression upon Hypoxia Is Regulated by RNA Editing. F11R is a cell adhesion molecule found on the surface of human platelets. It plays a role in platelet aggregation, cell migration and cell proliferation. F11R is subjected to RNA editing, a post-transcriptional modification which affects RNA structure, stability, localization, translation and splicing. RNA editing in the 3'UTR of F11R and RNA levels are increased upon hypoxia. We therefore set to examine if RNA editing plays a role in the increase of F11R RNA seen upon hypoxic conditions. Figures Citation: Ben-Zvi M, Amariglio N, Paret G, Nevo-Caspi Y (2013) F11R Expression upon Hypoxia Is Regulated by RNA Editing.
Editor: Stefan Maas, NIGMS, NIH, United States of America Received: April 18, 2013; Accepted: September 12, 2013; Published: October 16, 2013 Copyright: © 2013 Ben-Zvi et al. Funding: Amisragaz is a non-medical and non-pharmaceutical Israeli company that philanthropically supports our Pediatric Intensive Care Department. Introduction Results Figure 1. Silencing of ADAR1 Figure 2. An RNA-Seq Transcriptome Analysis of Histone Modifiers and RNA Silencing Genes in Soybean during Floral Initiation Process. Introduction Flowering is a crucial process during the life cycle of plants which determines reproductive success in plant and underpins productivity in agriculture. Grains legumes including soybeans (Glycine max) are second only to cereal crops as a source of food and feed.
Soybean is one of the world’s most important crops, particularly for most of the worldwide oilseed production. In term of flowering characteristics, soybean is a short-day plant, nonvernalisation-responsive species, and flower reversion can be induced in soybean when plants are transferred from long-day to short-day condition. In addition, soybean cultivars from different maturity groups display variability in the photoperiod (and/or temperature) stimulus requirements for the initiation of flowering [1]. In eukaryotic cells, the genetic information is stored in chromatin which is organised in nucleosome units composed of histone proteins that are wrapped by highly compacted DNA.
Figure 1. Figure 2. Figure 3. The Mitochondrial RNA Landscape of Saccharomyces cerevisiae. Mitochondria are essential organelles that harbor a reduced genome, and expression of that genome requires regulated metabolism of its transcriptome by nuclear-encoded proteins. Despite extensive investigation, a comprehensive map of the yeast mitochondrial transcriptome has not been developed and all of the RNA-metabolizing proteins have not been identified, both of which are prerequisites to elucidating the basic RNA biology of mitochondria. Here, we present a mitochondrial transcriptome map of the yeast S288C reference strain.
Using RNAseq and bioinformatics, we show the expression level of all transcripts, revise all promoter, origin of replication, and tRNA annotations, and demonstrate for the first time the existence of alternative splicing, mirror RNAs, and a novel RNA processing site in yeast mitochondria. The transcriptome map has revealed new aspects of mitochondrial RNA biology and we expect it will serve as a valuable resource. Figures Copyright: © 2013 Turk et al. RNAseq. Use of a Capture-Based Pathogen Transcript Enrichment Strategy for RNA-Seq Analysis of the Francisella Tularensis LVS Transcriptome during Infection of Murine Macrophages. The Long Noncoding RNA HOTAIR Contributes to Cisplatin Resistance of Human Lung Adenocarcinoma Cells via downregualtion of p21WAF1/CIP1 Expression. Viral RNA Levels and env Variants in Semen and Tissues of Mature Male Rhesus Macaques Infected with SIV by Penile Inoculation.
Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development. Variation of Transaminases, HCV-RNA Levels and Th1/Th2 Cytokine Production during the Post-Partum Period in Pregnant Women with Chronic Hepatitis C. Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses.
Inheritable and Precise Large Genomic Deletions of Non-Coding RNA Genes in Zebrafish Using TALENs. RNA-Seq Reveals Differential Gene Expression in Staphylococcus aureus with Single-Nucleotide Resolution. Characterization of the Mechanism of Inhibin α-Subunit Gene in Mouse Anterior Pituitary Cells by RNA Interference. Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-Sequence Retaining Transcripts in Mouse and Rat Neurons. An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme. The Role of Hydrogen Peroxide and Nitric Oxide in the Induction of Plant-Encoded RNA-Dependent RNA Polymerase 1 in the Basal Defense against Tobacco Mosaic Virus.
Revealing of Mycobacterium marinum Transcriptome by RNA-seq. Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells. Small RNA Profiling of Influenza A Virus-Infected Cells Identifies miR-449b as a Regulator of Histone Deacetylase 1 and Interferon Beta. CpG Usage in RNA Viruses: Data and Hypotheses. High-Throughput RNA FISH Analysis by Imaging Flow Cytometry Reveals That Pioneer Factor Foxa1 Reduces Transcriptional Stochasticity. Evaluation of Digital PCR for Absolute RNA Quantification. Sliding over the Blocks in Enzyme-Free RNA Copying – One-Pot Primer Extension in Ice. Evidence for DNA Cleavage Caused Directly by a transfer RNA-Targeting Toxin. Turbo FISH: A Method for Rapid Single Molecule RNA FISH. A Pre-mRNA-Splicing Factor Is Required for RNA-Directed DNA Methylation in Arabidopsis.
Internal Ribosome Entry Segment Activity of ATXN8 Opposite Strand RNA. Use of Recombinant Tobacco Mosaic Virus To Achieve RNA Interference in Plants against the Citrus Mealybug, Planococcus citri (Hemiptera: Pseudococcidae) Transcript Assembly and Quantification by RNA-Seq Reveals Differentially Expressed Genes between Soft-Endocarp and Hard-Endocarp Hawthorns. Cell-Type Specific Features of Circular RNA Expression. The HIV-1 Nef Protein Binds Argonaute-2 and Functions as a Viral Suppressor of RNA Interference. RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici. Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells.
New Preclinical Antimalarial Drugs Potently Inhibit Hepatitis C Virus Genotype 1b RNA Replication. Characterization and Comparative Analyses of Muscle Transcriptomes in Dorper and Small-Tailed Han Sheep Using RNA-Seq Technique. Sphingosine Kinase 1 Serves as a Pro-Viral Factor by Regulating Viral RNA Synthesis and Nuclear Export of Viral Ribonucleoprotein Complex upon Influenza Virus Infection. Differential Sensitivity of Bat Cells to Infection by Enveloped RNA Viruses: Coronaviruses, Paramyxoviruses, Filoviruses, and Influenza Viruses.
Reversible and Rapid Transfer-RNA Deactivation as a Mechanism of Translational Repression in Stress. Identification of MiRNA from Eggplant (Solanum melongena L.) by Small RNA Deep Sequencing and Their Response to Verticillium dahliae Infection. Predicting Helical Topologies in RNA Junctions as Tree Graphs. RNA-Mediated Gene Silencing of Nicotinamide N-Methyltransferase Is Associated with Decreased Tumorigenicity in Human Oral Carcinoma Cells. Evidence for Multiple Distinct Interactions between Hepatitis B Virus P Protein and Its Cognate RNA Encapsidation Signal during Initiation of Reverse Transcription. The Mini-Chromosome Maintenance (Mcm) Complexes Interact with DNA Polymerase α-Primase and Stimulate Its Ability to Synthesize RNA Primers. Mediator Directs Co-transcriptional Heterochromatin Assembly by RNA Interference-Dependent and -Independent Pathways.
QTL Analysis of High Thermotolerance with Superior and Downgraded Parental Yeast Strains Reveals New Minor QTLs and Converges on Novel Causative Alleles Involved in RNA Processing. A Novel High Throughput Biochemical Assay to Evaluate the HuR Protein-RNA Complex Formation. RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level. Specific Inhibition of Tumor Cells by Oncogenic EGFR Specific Silencing by RNA interference. Conditional Knockout of Tumor Overexpressed Gene in Mouse Neurons Affects RNA Granule Assembly, Granule Translation, LTP and Short Term Habituation.
RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas. Manipulation of the Porcine Epidemic Diarrhea Virus Genome Using Targeted RNA Recombination. Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization. HIV-1 Tropism Testing in Subjects Achieving Undetectable HIV-1 RNA: Diagnostic Accuracy, Viral Evolution and Compartmentalization. Quality Control of RNA Preservation and Extraction from Paraffin-Embedded Tissue: Implications for RT-PCR and Microarray Analysis.
Recombinant Prion Protein Refolded with Lipid and RNA Has the Biochemical Hallmarks of a Prion but Lacks In Vivo Infectivity. Genome-Wide Analysis of Small RNA and Novel MicroRNA Discovery during Fiber and Seed Initial Development in Gossypium hirsutum. L. Comparative Study of Two Box H/ACA Ribonucleoprotein Pseudouridine-Synthases: Relation between Conformational Dynamics of the Guide RNA, Enzyme Assembly and Activity. Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge. Tracing the Transcriptomic Changes in Synthetic Trigenomic allohexaploids of Brassica Using an RNA-Seq Approach.
The Arabidopsis RNA Binding Protein with K Homology Motifs, SHINY1, Interacts with the C-terminal Domain Phosphatase-like 1 (CPL1) to Repress Stress-Inducible Gene Expression. The RNA-binding Proteins FMR1, Rasputin and Caprin Act Together with the UBA Protein Lingerer to Restrict Tissue Growth in Drosophila melanogaster. Transfection of Infectious RNA and DNA/RNA Layered Vectors of Semliki Forest Virus by the Cell-Penetrating Peptide Based Reagent PepFect6. RNA Sequencing of the Human Milk Fat Layer Transcriptome Reveals Distinct Gene Expression Profiles at Three Stages of Lactation. RNA-Interference Components Are Dispensable for Transcriptional Silencing of the Drosophila Bithorax-Complex. An O Island 172 Encoded RNA Helicase Regulates the Motility of Escherichia coli O157:H7.
A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples. Vaccination with Recombinant RNA Replicon Particles Protects Chickens from H5N1 Highly Pathogenic Avian Influenza Virus. Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans.