- Mapping and quantifying mammalian transcriptomes by RNA-Seq
Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
Nat Methods 5:621-8. 2008
..by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq)...
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G Grabherr
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 29:644-52. 2011
..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
- RNA-Seq: a revolutionary tool for transcriptomics
Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520, USA
Nat Rev Genet 10:57-63. 2009
b>RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes...
- RNA-guided human genome engineering via Cas9
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Science 339:823-6. 2013
..clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids...
- Mfold web server for nucleic acid folding and hybridization prediction
Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
Nucleic Acids Res 31:3406-15. 2003
..The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large...
- Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction
Anal Biochem 162:156-9. 1987
A new method of total RNA isolation by a single extraction with an acid guanidinium thiocyanate-phenol-chloroform mixture is described...
- A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
Science 337:816-21. 2012
..in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA...
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Department of Computer Sciences, University of Wisconsin Madison, Madison, WI, USA
BMC Bioinformatics 12:323. 2011
b>RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms...
- Initial sequencing and analysis of the human genome
E S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001
..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
- A scaling normalization method for differential expression analysis of RNA-seq data
Mark D Robinson
Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Australia
Genome Biol 11:R25. 2010
The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA...
- DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua, University, Beijing 100084, China
Bioinformatics 26:136-8. 2010
High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform...
- Infernal 1.0: inference of RNA alignments
Eric P Nawrocki
HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
Bioinformatics 25:1335-7. 2009
INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence ..
- A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
Cell 146:353-8. 2011
..We propose that this "competing endogenous RNA" (ceRNA) activity forms a large-scale regulatory network across the transcriptome, greatly expanding the functional ..
- RNA sequencing: advances, challenges and opportunities
Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA
Nat Rev Genet 12:87-98. 2011
In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes...
- De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J Haas
Broad Institute of Massachusetts Institute of Technology MIT, Cambridge, Massachusetts, USA
Nat Protoc 8:1494-512. 2013
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary ..
- Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers
Department of Neurology, Massachusetts General Hospital, and Neuroscience Program, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
Nat Cell Biol 10:1470-6. 2008
..Messenger RNA mutant/variants and miRNAs characteristic of gliomas could be detected in serum microvesicles of glioblastoma ..
- The Vienna RNA websuite
Andreas R Gruber
Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
Nucleic Acids Res 36:W70-4. 2008
The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package...
- The RIN: an RNA integrity number for assigning integrity values to RNA measurements
Agilent Technologies, Hewlett Packard Strasse 8, 76337 Waldbronn, Germany
BMC Mol Biol 7:3. 2006
The integrity of RNA molecules is of paramount importance for experiments that try to reflect the snapshot of gene expression at the moment of RNA extraction...
- Natural RNA circles function as efficient microRNA sponges
Thomas B Hansen
Department of Molecular Biology and Genetics, Aarhus University, C F Møllers Allé 3, 8000C, Aarhus, Denmark
Nature 495:384-8. 2013
..has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants...
- Rfam: updates to the RNA families database
Paul P Gardner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
Nucleic Acids Res 37:D136-40. 2009
Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs)...
- Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
Genome Biol 3:RESEARCH0034. 2002
- Detecting differential usage of exons from RNA-seq data
European Molecular Biology Laboratory, 69111 Heidelberg, Germany
Genome Res 22:2008-17. 2012
b>RNA-seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression...
- RNA maps reveal new RNA classes and a possible function for pervasive transcription
Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
Science 316:1484-8. 2007
Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential...
- Computation for ChIP-seq and RNA-seq studies
Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA
Nat Methods 6:S22-32. 2009
..of protein-DNA interactions and transcriptomes are increasingly done by deep DNA sequencing methods (ChIP-seq and RNA-seq)...
- Analysis and design of RNA sequencing experiments for identifying isoform regulation
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology MIT, Cambridge, Massachusetts, USA
Nat Methods 7:1009-15. 2010
..To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of ..
- Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
A E Pasquinelli
Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
Nature 408:86-9. 2000
..Transition from the first to the second larval stage fates requires the 22-nucleotide lin-4 RNA, and transition from late larval to adult cell fates requires the 21-nucleotide let-7 RNA...
- Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends
Claus M Azzalin
Swiss Institute for Experimental Cancer Research ISREC, CH 1066 Epalinges, Switzerland
Science 318:798-801. 2007
..We demonstrate that mammalian telomeres are transcribed into telomeric repeat-containing RNA (TERRA)...
- RNA and disease
Thomas A Cooper
Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
Cell 136:777-93. 2009
Cellular functions depend on numerous protein-coding and noncoding RNAs and the RNA-binding proteins associated with them, which form ribonucleoprotein complexes (RNPs)...
- Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila
Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
Cell 128:1089-103. 2007
..Thus, sense piRNAs, formed following cleavage of transposon mRNAs may enhance production of antisense piRNAs, complementary to active elements, by directing cleavage of transcripts from master control loci...
- tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
T M Lowe
Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
Nucleic Acids Res 25:955-64. 1997
We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases...
- Functions and regulation of RNA editing by ADAR deaminases
Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania 19104 4268, USA
Annu Rev Biochem 79:321-49. 2010
One type of RNA editing converts adenosines to inosines (A-->I editing) in double-stranded RNA (dsRNA) substrates. A-->I RNA editing is mediated by adenosine deaminase acting on RNA (ADAR) enzymes...
- Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 458:223-7. 2009
..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
- VARNA: Interactive drawing and editing of the RNA secondary structure
LRI, UMR CNRS 8623, UMR CNRS 8621, Universite Paris Sud 11, F91405 Orsay Cedex, France
Bioinformatics 25:1974-5. 2009
VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
- MODOMICS: a database of RNA modification pathways--2013 update
Magdalena A Machnicka
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 109 Warsaw, Poland
Nucleic Acids Res 41:D262-7. 2013
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in ..
- Modelling and simulating generic RNA-Seq experiments with the flux simulator
Bioinformatics and Genomics Program, Centre de Regulacio Genomica CRG, 08003 Barcelona, Spain
Nucleic Acids Res 40:10073-83. 2012
High-throughput sequencing of cDNA libraries constructed from cellular RNA complements (RNA-Seq) naturally provides a digital quantitative measurement for every expressed RNA molecule...
- RNAstructure: software for RNA secondary structure prediction and analysis
Jessica S Reuter
Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
BMC Bioinformatics 11:129. 2010
To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides...
- RSeQC: quality control of RNA-seq experiments
Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
Bioinformatics 28:2184-5. 2012
b>RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses...
- Identification of novel genes coding for small expressed RNAs
Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
Science 294:853-8. 2001
..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
- Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica and Instituto Nacional de Bioinformatica, Parc Cientific de Barcelona, Barcelona 08028, Spain
Biophys J 92:3817-29. 2007
..The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution...
- Vienna RNA secondary structure server
Ivo L Hofacker
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
Nucleic Acids Res 31:3429-31. 2003
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures...
- Statistical inferences for isoform expression in RNA-Seq
Institute for Computational and Mathematical Engineering and Department of Statistics, Stanford University, Stanford, CA 94305, USA
Bioinformatics 25:1026-32. 2009
The development of RNA sequencing (RNA-Seq) makes it possible for us to measure transcription at an unprecedented precision and throughput...
- Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
BGI Shenzhen, Shenzhen, China
Nat Biotechnol 30:253-60. 2012
b>RNA editing is a post-transcriptional event that recodes hereditary information...
- Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
Gregory R Grant
Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Bioinformatics 27:2518-28. 2011
..Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing...
- Extension of life-span by introduction of telomerase into normal human cells
A G Bodnar
Geron Corporation, Menlo Park, CA 94025, USA
Science 279:349-52. 1998
..The ability to maintain normal human cells in a phenotypically youthful state could have important applications in research and medicine...
- From RNA-seq reads to differential expression results
Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
Genome Biol 11:220. 2010
Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
- The transcriptional landscape of the mammalian genome
Science 309:1559-63. 2005
..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
- Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs
Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
Mol Cell 15:185-97. 2004
..Exogenously introduced siRNAs also associate with Ago2 for guiding target RNA cleavage...
- T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
Paolo Di Tommaso
Centre For Genomic Regulation Pompeu Fabra University, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
Nucleic Acids Res 39:W13-7. 2011
..available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using ..
- Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390 9152, USA
Cell 149:753-67. 2012
Eukaryotic cells contain assemblies of RNAs and proteins termed RNA granules. Many proteins within these bodies contain KH or RRM RNA-binding domains as well as low complexity (LC) sequences of unknown function...
- Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence
Waksman Institute, Piscataway, NJ 08854, USA
Proc Natl Acad Sci U S A 108:10098-103. 2011
..sequences) systems provide adaptive immunity against viruses when a spacer sequence of small CRISPR RNA (crRNA) matches a protospacer sequence in the viral genome...
- RNA integrity and the effect on the real-time qRT-PCR performance
Physiology Weihenstephan, Center of Life and Food Sciences ZIEL, Technical University of Munich, 85350 Freising, Germany
Mol Aspects Med 27:126-39. 2006
The assessment of RNA integrity is a critical first step in obtaining meaningful gene expression data...
- UNAFold: software for nucleic acid folding and hybridization
Nicholas R Markham
Xerox Litigation Services, Albany, NY, USA
Methods Mol Biol 453:3-31. 2008
..Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling...
- Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Mol Cell 44:667-78. 2011
Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown...
- RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions
Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 108:10092-7. 2011
Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids...
- DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration
Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky 40506, USA
Nature 471:325-30. 2011
..DICER1 knockdown induces accumulation of Alu RNA in human RPE cells and Alu-like B1 and B2 RNAs in mouse RPE...
- The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression
Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, Zurich, Switzerland
FEBS J 272:2118-31. 2005
The RNA recognition motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes...
- Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex
Debora Lika Makino
Department of Structural Cell Biology, MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
Nature 495:70-5. 2013
The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44...
- Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9
Jian Feng Li
Nat Biotechnol 31:688-91. 2013
- Transcriptional profiling of bovine milk using RNA sequencing
Department of Animal Science, University of California Davis, CA, 95616 8521, USA
BMC Genomics 13:45. 2012
..expressed in milk somatic cells of transition (day 15), peak (day 90) and late (day 250) lactation Holstein cows by RNA sequencing...
- The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA
BMC Biol 8:149. 2010
..However, the fraction of all cellular RNA whose function we do not understand and the fraction of the genome that is utilized to produce that RNA remain ..
- RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing
Brian T Wilhelm
Laboratory of Molecular Genetics of Stem Cells, C P 6128 Succursale Centre Ville, Montreal, Que H3C3J7, Canada
Methods 48:249-57. 2009
..One such method that has recently been developed uses MPS technology to directly survey the RNA content of cells, without requiring any of the traditional cloning associated with EST sequencing...
- G-quadruplexes in RNA biology
INSERM UMR 1037, University of Toulouse III, Cancer Research Center of Toulouse, Toulouse 31432, Cedex 4, France
Wiley Interdiscip Rev RNA 3:495-507. 2012
G-quadruplexes are noncanonical structures formed by G-rich DNA and RNA sequences that fold into a four-stranded conformation...
- Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
Mol Cell 42:794-805. 2011
We present a molecular dissection of pause site-dependent transcriptional termination for mammalian RNA polymerase II (Pol II)-transcribed genes...
- ExoCarta 2012: database of exosomal proteins, RNA and lipids
Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
Nucleic Acids Res 40:D1241-4. 2012
..ExoCarta (http://www.exocarta.org) is a manually curated database of exosomal proteins, RNA and lipids. The database catalogs information from both published and unpublished exosomal studies...
- RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway
Yu Hsin Chiu
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9148, USA
Cell 138:576-91. 2009
..mitochondrial antiviral signaling (MAVS) proteins mediate IFN production in response to cytosolic double-stranded RNA or single-stranded RNA containing 5'-triphosphate (5'-ppp)...
- Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction
Stephen A Bustin
Centre for Academic Surgery Institute of Cell and Molecular Science Barts, University of London, UK
J Biomol Tech 15:155-66. 2004
Polymerase chain reaction (PCR)-based assays can target either DNA (the genome) or RNA (the transcriptome). Targeting the genome generates robust data that are informative and, most importantly, generally applicable...
- Infernal 1.1: 100-fold faster RNA homology searches
Eric P Nawrocki
HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
Bioinformatics 29:2933-5. 2013
Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input...
- Incorporating RNA-seq data into the zebrafish Ensembl genebuild
John E Collins
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Genome Res 22:2067-78. 2012
..of gene models is improved by increasing the species-specific component that can be cost-effectively achieved using RNA-seq. Two zebrafish gene annotations are presented in Ensembl version 62 built on the Zv9 reference sequence...
- De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology
Jacob E Crawford
Department of Entomology, Cornell University, Ithaca, New York, United States of America
PLoS ONE 5:e14202. 2010
..funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform...
- Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
Nat Biotechnol 29:607-14. 2011
Mammalian RNA complexity is regulated through interactions of RNA-binding proteins (RBPs) with their target transcripts...
- Uncovering the complexity of transcriptomes with RNA-Seq
Institute of Genetics and Biophysics A Buzzati Traverso, IGB CNR, Naples, Italy
J Biomed Biotechnol 2010:853916. 2010
..b>RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide ..
- RNAalifold: improved consensus structure prediction for RNA alignments
Stephan H Bernhart
Department of Computer Science, University of Leipzig, Leipzig, Germany
BMC Bioinformatics 9:474. 2008
..In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach...
- RNA processing and its regulation: global insights into biological networks
Donny D Licatalosi
Howard Hughes Medical Institute, Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York 10021, USA
Nat Rev Genet 11:75-87. 2010
..of eukaryotic gene expression have been transformed by the finding that enormous diversity can be generated at the RNA level...
- Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
Nature 456:921-6. 2008
..Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step...
- RNA recognition motifs: boring? Not quite
Institute for Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
Curr Opin Struct Biol 18:290-8. 2008
The RNA recognition motif (RRM) is one of the most abundant protein domains in eukaryotes...
- The application of DNA and RNA G-quadruplexes to therapeutic medicines
Gavin W Collie
CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, UK WC1N 1AX
Chem Soc Rev 40:5867-92. 2011
..We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets...
- Local RNA translation at the synapse and in disease
Department of Pharmacology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
J Neurosci 31:16086-93. 2011
..mRNA binding proteins (RBPs), such as FMRP, function as key regulators of local RNA translation, and the mTORC1 pathway acts as a primary signaling cascade for regulation of these proteins...
- 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
Yan W Asmann
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
BMC Genomics 10:531. 2009
..Currently there are two protocols: full-length RNA sequencing (RNA-SEQ) and 3'-tag digital gene expression (DGE)...
- Prediction of protein-RNA binding sites by a random forest method with combined features
Zhi Ping Liu
Key Laboratory of Systems Biology, SIBS Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
Bioinformatics 26:1616-22. 2010
Protein-RNA interactions play a key role in a number of biological processes, such as protein synthesis, mRNA processing, mRNA assembly, ribosome function and eukaryotic spliceosomes...
- Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping
Wuhan University, Hubei, China
Mol Cell 36:996-1006. 2009
..indicates that > 90% of human genes undergo alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells...
- Geometric nomenclature and classification of RNA base pairs
N B Leontis
Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Ohio 43403, USA
RNA 7:499-512. 2001
Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition...
- Accurate SHAPE-directed RNA structure determination
Katherine E Deigan
Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599 3290, USA
Proc Natl Acad Sci U S A 106:97-102. 2009
..Deducing these structure-function relationships requires that it be possible to predict RNA secondary structures accurately...
- ExoCarta: A compendium of exosomal proteins and RNA
Joint ProteomicS Laboratory, Ludwig Institute for Cancer Research and The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
Proteomics 9:4997-5000. 2009
..Here, we describe ExoCarta, a compendium for proteins and RNA molecules identified in exosomes...
- Modeling non-uniformity in short-read rates in RNA-Seq data
Department of Statistics, Stanford University, Sequoia Hall, 390 Serra Mall, Stanford, CA 94305, USA
Genome Biol 11:R50. 2010
After mapping, RNA-Seq data can be summarized by a sequence of read counts commonly modeled as Poisson variables with constant rates along each transcript, which actually fit data poorly...
- The RNA Modification Database, RNAMDB: 2011 update
William A Cantara
The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
Nucleic Acids Res 39:D195-201. 2011
Since its inception in 1994, The RNA Modification Database (RNAMDB, http://rna-mdb.cas.albany.edu/RNAmods/) has served as a focal point for information pertaining to naturally occurring RNA modifications...
- Facile means for quantifying microRNA expression by real-time PCR
North Carolina State University, Raleigh, NC 27695 7247, USA
Biotechniques 39:519-25. 2005
..Here we report a simple and sensitive real-time PCR method for quantifying the expression of plant miRNAs. Total RNA, including miRNAs, was polyadenylated and reverse-transcribed with a poly(T) adapter into cDNAs for real-time PCR ..
- Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure
Integrative Biology Section, The University of Texas at Austin, Austin, TX 78712, USA
Mol Ecol 20:3599-616. 2011
..Here, we applied a novel RNA-Seq protocol to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef-..
- Exosome isolation for proteomic analyses and RNA profiling
Douglas D Taylor
James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
Methods Mol Biol 728:235-46. 2011
..Recently, we have demonstrated the presence of miRNAs within the RNA fraction of circulating tumor-derived exosomes...
- Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition
Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
Proc Natl Acad Sci U S A 109:9396-401. 2012
..Hfq forms hexameric rings, which preferably bind uridine-rich RNA 3' ends on their proximal surface and adenine-rich sequences on their distal surface...
- Organization of intracellular reactions with rationally designed RNA assemblies
Camille J Delebecque
Harvard Medical School, Department of Systems Biology, 200 Longwood Avenue, Boston, MA 02115, USA
Science 333:470-4. 2011
..We designed and assembled multidimensional RNA structures and used them as scaffolds for the spatial organization of bacterial metabolism...
- Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 29:436-42. 2011
Cellular RNA levels are determined by the interplay of RNA production, processing and degradation...
- Exporting RNA from the nucleus to the cytoplasm
Biochemie Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
Nat Rev Mol Cell Biol 8:761-73. 2007
The transport of RNA molecules from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes via mobile export receptors...
- RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform
C Frank Bennett
Isis Pharmaceuticals, Inc, Carlsbad, California 92008, USA
Annu Rev Pharmacol Toxicol 50:259-93. 2010
Dramatic advances in understanding of the roles RNA plays in normal health and disease have greatly expanded over the past 10 years and have made it clear that scientists are only beginning to comprehend the biology of RNAs...
- RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)
Edward J Merino
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 3290, USA
J Am Chem Soc 127:4223-31. 2005
The reactivity of an RNA ribose hydroxyl is shown to be exquisitely sensitive to local nucleotide flexibility because a conformationally constrained adjacent 3'-phosphodiester inhibits formation of the deprotonated, nucleophilic oxyanion ..
- RNA nucleotide methylation
Laboratoire ARN RNP Maturation Structure Fonction, Enzymologie Moléculaire et Structurale AREMS, Universite Henri Poincare, Vandoeuvre les Nancy, France
Wiley Interdiscip Rev RNA 2:611-31. 2011
Methylation of RNA occurs at a variety of atoms, nucleotides, sequences and tertiary structures...
- RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability
Howard Hughes Medical Institute Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Mol Cell 44:978-88. 2011
..Studies in yeast and mammalian cells have shown that DSBs and instability can occur through RNA:DNA hybrids generated by defects in RNA elongation and splicing...
- Prediction of RNA secondary structure using generalized centroid estimators
Mizuho Information and Research Institute, Inc, 2 3 Kanda Nishikicho, Chiyoda ku, Tokyo 101 8443, Japan
Bioinformatics 25:465-73. 2009
..However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures...
- Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq
Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA
RNA 16:1610-22. 2010
- Ribozyme-catalyzed transcription of an active ribozyme
Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Science 332:209-12. 2011
A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of replicating a primordial RNA "genome...
- Role of RNA structure in regulating pre-mRNA splicing
M Bryan Warf
Institute of Molecular Biology, and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
Trends Biochem Sci 35:169-78. 2010
Pre-mRNA splicing involves removing non-coding introns from RNA transcripts. It is carried out by the spliceosome, along with other auxiliary factors...
- Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension
Cardiovascular Institute, Univ of Pittsburgh, PA 15213 2582, USA
Am J Physiol Heart Circ Physiol 298:H1235-48. 2010
..Using genomewide microarray analysis, we generated the largest data set to date of RNA expression profiles from lung tissue specimens from 1) 18 PAH subjects and 2) 8 subjects with PH secondary to ..