251
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Frey BJ, Morris QD, Hughes TR. GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data. J Comput Biol 2006; 13:200-14. [PMID: 16597235 DOI: 10.1089/cmb.2006.13.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genome-wide microarray designs containing millions to hundreds of millions of probes are available for a variety of mammals, including mouse and human. These genome tiling arrays can potentially lead to significant advances in science and medicine, e.g., by indicating new genes and alternative primary and secondary transcripts. While bottom-up pattern matching techniques (e.g., hierarchical clustering) can be used to find gene structures in microarray data, we believe the many interacting hidden variables and complex noise patterns more naturally lead to an analysis based on generative models. We describe a generative model of tiling data and show how the sum-product algorithm can be used to infer hybridization noise, probe sensitivity, new transcripts, and alternative transcripts. The method, called GenRate, maximizes a global scoring function that enables multiple transcripts to compete for ownership of putative probes. We apply GenRate to a new exon tiling dataset from mouse chromosome 4 and show that it makes significantly more predictions than a previously described hierarchical clustering method at the same false positive rate. GenRate correctly predicts many known genes and also predicts new gene structures. As new problems arise, additional hidden variables can be incorporated into the model in a principled fashion, so we believe that GenRate will prove to be a useful tool in the new era of genome-wide tiling microarray analysis.
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Affiliation(s)
- Brendan J Frey
- Department of Electrical and Computer Engineering, University of Toronto, Ontario, Canada.
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252
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Abstract
Temperature is an important parameter that free-living cells monitor constantly. The expression of heat-shock, cold-shock and some virulence genes is coordinated in response to temperature changes. Apart from protein-mediated transcriptional control mechanisms, translational control by RNA thermometers is a widely used regulatory strategy. RNA thermometers are complex RNA structures that change their conformation in response to temperature. Most, but not all, RNA thermometers are located in the 5'-untranslated region and mask ribosome-binding sites by base pairing at low temperatures. Melting of the structure at increasing temperature permits ribosome access and translation initiation. Different cis-acting RNA thermometers and a trans-acting thermometer will be presented.
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Affiliation(s)
- Franz Narberhaus
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Bochum, Germany.
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253
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Haider S, Matsumoto R, Kurosawa N, Wakui K, Fukushima Y, Isobe M. Molecular characterization of a novel translocation t(5;14)(q21;q32) in a patient with congenital abnormalities. J Hum Genet 2006; 51:335-340. [PMID: 16498521 DOI: 10.1007/s10038-006-0365-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Accepted: 12/18/2005] [Indexed: 11/30/2022]
Abstract
Chromosomal translocations are frequently found to be associated with various malignant disorders as well as congenital abnormalities. We report the characterization of a novel reciprocal translocation t(5;14)(q21;q32) in a patient with congenital abnormalities manifested by severe mental retardation, athetotic tetraplegia, microcephaly, peculiar facies (upward slanting of palpebral fissures), clinodactyly of the fifth fingers, and overlapping toes. Using a JHGP24 lymphoblast cell line derived from this patient, metaphase fluorescence in situ hybridization with bacterial artificial chromosome and cosmid probes and subsequent molecular analysis mapped the translocation breakpoint to the nucleotide level. Sequence analysis of the breakpoint junctions revealed the presence of a homologous sequence, GTGGC, along with a single nucleotide substitution and an insertion in der(14), and a single nucleotide deletion in the der(5) chromosome. We also attempted to identify and characterize the transcripts near the breakpoint by 5' and 3' rapid amplification of cDNA ends. Although we found several transcripts near the breakpoint of chromosome 14, the lack of significant ORFs within these transcripts suggests they are likely to be non-coding RNAs. These transcripts may have an important role in the neurogenesis or differentiation.
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MESH Headings
- Adult
- Base Sequence
- Blotting, Southern
- Cell Line
- Chromosome Breakage
- Chromosomes, Artificial, Bacterial
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 5
- Clone Cells
- Cloning, Molecular
- Congenital Abnormalities/genetics
- Conserved Sequence
- Cosmids
- DNA Probes
- DNA, Complementary/genetics
- Female
- Humans
- In Situ Hybridization, Fluorescence
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Amplification Techniques
- Physical Chromosome Mapping
- Restriction Mapping
- Sequence Deletion
- Translocation, Genetic
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Affiliation(s)
- Shawkat Haider
- Laboratory of Molecular and Cellular Biology, Department of Materials and Biosystem Engineering, Faculty of Engineering, Toyama University, 3190 Gofuku, Toyama 930-8555, Japan
| | - Rie Matsumoto
- Laboratory of Molecular and Cellular Biology, Department of Materials and Biosystem Engineering, Faculty of Engineering, Toyama University, 3190 Gofuku, Toyama 930-8555, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Department of Materials and Biosystem Engineering, Faculty of Engineering, Toyama University, 3190 Gofuku, Toyama 930-8555, Japan
| | - Keiko Wakui
- Department of Medical Genetics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan
| | - Yoshimitsu Fukushima
- Department of Medical Genetics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Department of Materials and Biosystem Engineering, Faculty of Engineering, Toyama University, 3190 Gofuku, Toyama 930-8555, Japan.
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254
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Affiliation(s)
- Paul D Berk
- The Division of Digestive Liver Diseases, Department of Medicine, Columbia University Medical Center, New York, NY
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255
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Hüttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 2006; 34:635-46. [PMID: 16436800 PMCID: PMC1351373 DOI: 10.1093/nar/gkj469] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 12/12/2022] Open
Abstract
Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until recent genome-wide searches discovered thousands of these molecules and their genes in a variety of model organisms. Some of these screens were based on biocomputational prediction of ncRNA candidates within entire genomes of model organisms. Alternatively, direct biochemical isolation of expressed ncRNAs from cells, tissues or entire organisms has been shown to be a powerful approach to identify ncRNAs both at the level of individual molecules and at a global scale. In this review, we will survey several such wet-lab strategies, i.e. direct sequencing of ncRNAs, shotgun cloning of small-sized ncRNAs (cDNA libraries), microarray analysis and genomic SELEX to identify novel ncRNAs, and discuss the advantages and limits of these approaches.
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Affiliation(s)
- Alexander Hüttenhofer
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria.
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256
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Carrasco N, Caton-Williams J, Brandt G, Wang S, Huang Z. Efficient Enzymatic Synthesis of Phosphoroselenoate RNA by Using Adenosine 5′-(α-P-Seleno)triphosphate. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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257
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Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA. Features of Arabidopsis genes and genome discovered using full-length cDNAs. PLANT MOLECULAR BIOLOGY 2006; 60:69-85. [PMID: 16463100 DOI: 10.1007/s11103-005-2564-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2004] [Accepted: 08/29/2005] [Indexed: 05/06/2023]
Abstract
Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5'-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3'-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5'-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper.
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258
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Pekarsky Y, Calin GA, Aqeilan R. Chronic lymphocytic leukemia: molecular genetics and animal models. Curr Top Microbiol Immunol 2005; 294:51-70. [PMID: 16323427 DOI: 10.1007/3-540-29933-5_4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chronic lymphocytic leukemia accounts for almost 30% of all adult leukemia cases in the United States and Western Europe. Although several common genomic abnormalities in CLL have been identified, mutational and functional analysis of corresponding genes so far have not proved their involvement in CLL. Our latest studies demonstrated functional involvement of Tcl1 oncoprotein and microRNA genes in the pathogenesis of CLL. Deregulated expression of Tcl1 in transgenic mice resulted in CLL. These CLL tumors showed abnormalities in expression of murine microRNA genes mmu-mir-15a and mmu-mir-16-1. Interestingly, human homologs of these genes, mir-15a and mir-16-1, located at the chromosome 13q14 are also deleted in human CLL samples. In this review we summarize and discuss these new developments. These recently emerged insights into the molecular mechanisms of CLL will allow for the development of new approaches to treat this disease.
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MESH Headings
- Animals
- Chromosome Aberrations
- Disease Models, Animal
- Gene Expression Profiling
- Humans
- Leukemia, Experimental/etiology
- Leukemia, Experimental/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Mice
- MicroRNAs/genetics
- Models, Biological
- Molecular Biology
- Oncogene Protein v-akt/genetics
- Proto-Oncogene Proteins/genetics
- RNA, Neoplasm/genetics
- Signal Transduction
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Affiliation(s)
- Y Pekarsky
- Comprehensive Cancer Center, Ohio State University, Columbus 43210, USA
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259
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Arluison V, Mura C, Guzmán MR, Liquier J, Pellegrini O, Gingery M, Régnier P, Marco S. Three-dimensional structures of fibrillar Sm proteins: Hfq and other Sm-like proteins. J Mol Biol 2005; 356:86-96. [PMID: 16337963 DOI: 10.1016/j.jmb.2005.11.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2005] [Revised: 11/02/2005] [Accepted: 11/03/2005] [Indexed: 10/25/2022]
Abstract
Hfq is a nucleic acid-binding protein that functions as a global regulator of gene expression by virtue of its interactions with several small, non-coding RNA species. Originally identified as an Escherichia coli host factor required for RNA phage Qbeta replication, Hfq is now known to post-transcriptionally regulate bacterial gene expression by modulating both mRNA stability and translational activity. Recently shown to be a member of the diverse Sm protein family, Hfq adopts the OB-like fold typical of other Sm and Sm-like (Lsm) proteins, and also assembles into toroidal homo-oligomers that bind single-stranded RNA. Similarities between the structures, functions, and evolution of Sm/Lsm proteins and Hfq are continually being discovered, and we now report an additional, unexpected biophysical property that is shared by Hfq and other Sm proteins: E.coli Hfq polymerizes into well-ordered fibres whose morphologies closely resemble those found for Sm-like archaeal proteins (SmAPs). However, the hierarchical assembly of these fibres is dissimilar: whereas SmAPs polymerize into polar tubes (and striated bundles of such tubes) by head-to-tail stacking of individual homo-heptamers, helical Hfq fibres are formed by cylindrical slab-like layers that consist of 36 subunits arranged as a hexamer of Hfq homo-hexamers (i.e. protofilaments in a 6 x 6 arrangement). The different fibrillar ultrastructures formed by Hfq and SmAP are presented and examined herein, with the overall goal of elucidating another similarity amongst the diverse members of the Sm protein family.
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Affiliation(s)
- Véronique Arluison
- Institut de Biologie Physico-Chimique, CNRS UPR 9073 conventionnée avec l'université Paris 7, 13 rue P. et M. Curie, 75005 Paris, France.
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260
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Abstract
MOTIVATION Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. RESULTS In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. AVAILABILITY The source code is available under GNU Public License at the supplementary web site.
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Affiliation(s)
- Zasha Weinberg
- Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.
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261
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Laserson U, Gan HH, Schlick T. Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs. Nucleic Acids Res 2005; 33:6057-69. [PMID: 16254081 PMCID: PMC1270951 DOI: 10.1093/nar/gki911] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Riboswitches and RNA interference are important emerging mechanisms found in many organisms to control gene expression. To enhance our understanding of such RNA roles, finding small regulatory motifs in genomes presents a challenge on a wide scale. Many simple functional RNA motifs have been found by in vitro selection experiments, which produce synthetic target-binding aptamers as well as catalytic RNAs, including the hammerhead ribozyme. Motivated by the prediction of Piganeau and Schroeder [(2003) Chem. Biol., 10, 103–104] that synthetic RNAs may have natural counterparts, we develop and apply an efficient computational protocol for identifying aptamer-like motifs in genomes. We define motifs from the sequence and structural information of synthetic aptamers, search for sequences in genomes that will produce motif matches, and then evaluate the structural stability and statistical significance of the potential hits. Our application to aptamers for streptomycin, chloramphenicol, neomycin B and ATP identifies 37 candidate sequences (in coding and non-coding regions) that fold to the target aptamer structures in bacterial and archaeal genomes. Further energetic screening reveals that several candidates exhibit energetic properties and sequence conservation patterns that are characteristic of functional motifs. Besides providing candidates for experimental testing, our computational protocol offers an avenue for expanding natural RNA's functional repertoire.
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Affiliation(s)
- Uri Laserson
- Department of Chemistry, New York University251 Mercer Street, New York, NY 10012, USA
- Courant Institute of Mathematical Sciences, New York University251 Mercer Street, New York, NY 10012, USA
| | - Hin Hark Gan
- Department of Chemistry, New York University251 Mercer Street, New York, NY 10012, USA
| | - Tamar Schlick
- Department of Chemistry, New York University251 Mercer Street, New York, NY 10012, USA
- Courant Institute of Mathematical Sciences, New York University251 Mercer Street, New York, NY 10012, USA
- To whom correspondence should be addressed. Tel: +1 212 998 3116; Fax: +1 212 998 4152; E-mail:
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262
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Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res 2005; 33:5533-43. [PMID: 16204454 PMCID: PMC1243798 DOI: 10.1093/nar/gki852] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although both the 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs may play a crucial role in posttranscriptional gene regulation, we observe that cis-encoded natural antisense RNAs have a striking preferential complementarity to the 3'-UTRs of their target genes in mammalian (human and mouse) genomes. A null neutral model, evoking differences in the rate of 3'-UTR and 5'-UTR extension, could potentially explain high rates of 3'-to-3' overlap compared with 5'-to-5' overlap. However, employing a simulation model we show that this null model probably cannot explain the finding that 3'-to-3' overlapping pairs have a much higher probability (>5 times) of conservation in both mouse and human genomes with the same overlapping pattern than do 5'-to-5' overlaps. Furthermore, it certainly cannot explain the finding that overlapping pairs seen in both genomes have a significantly higher probability of having co-expression and inverse expression (i.e. characteristic of sense-antisense regulation) than do overlapping pairs seen in only one of the two species. We infer that the function of many 3'-to-3' overlaps is indeed antisense regulation. These findings underscore the preference for, and conservation of, 3'-UTR-targeted antisense regulation, and the importance of 3'-UTRs in gene regulation.
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Affiliation(s)
| | - Laurence D. Hurst
- Department of Biology and Biochemistry, University of BathSomerset, BA2 7AY, UK
| | - Gordon G. Carmichael
- Department of Genetics and Developmental Biology, University of Connecticut Health CenterFarmington, CT 06030-3301, USA
| | - Jianjun Chen
- To whom correspondence should be addressed. Tel: +1 773 795 5474; Fax: +1 773 702 3002;
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263
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Strippoli P, Canaider S, Noferini F, D'Addabbo P, Vitale L, Facchin F, Lenzi L, Casadei R, Carinci P, Zannotti M, Frabetti F. Uncertainty principle of genetic information in a living cell. Theor Biol Med Model 2005; 2:40. [PMID: 16197549 PMCID: PMC1262781 DOI: 10.1186/1742-4682-2-40] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 09/30/2005] [Indexed: 11/30/2022] Open
Abstract
Background Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming the genotype of a given living cell be known with absolute certainty so that the cell's behaviour (phenotype) can be correlated to that genetic information? To answer this question, we propose a series of thought experiments. Results We show that the genome sequence of any actual living cell cannot physically be known with absolute certainty, independently of the method used. There is an associated uncertainty, in terms of base pairs, equal to or greater than μs (where μ is the mutation rate of the cell type and s is the cell's genome size). Conclusion This finding establishes an "uncertainty principle" in genetics for the first time, and its analogy with the Heisenberg uncertainty principle in physics is discussed. The genetic information that makes living cells work is thus better represented by a probabilistic model rather than as a completely defined object.
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Affiliation(s)
- Pierluigi Strippoli
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Silvia Canaider
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Francesco Noferini
- Department of Physics, University of Bologna, Via Irnerio 46, 40126 Bologna (BO), Italy; Sezione INFN, Bologna, Italy
| | - Pietro D'Addabbo
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
- Dipartimento di Genetica e Microbiologia, University of Bari, 70126 Bari, Italy
| | - Lorenza Vitale
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Federica Facchin
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Luca Lenzi
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Raffaella Casadei
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Paolo Carinci
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Maria Zannotti
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Flavia Frabetti
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
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264
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Sharin E, Schein A, Mann H, Ben-Asouli Y, Jarrous N. RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis. Nucleic Acids Res 2005; 33:5120-32. [PMID: 16155184 PMCID: PMC1201335 DOI: 10.1093/nar/gki828] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli ribonuclease P (RNase P) has a protein component, termed C5, which acts as a cofactor for the catalytic M1 RNA subunit that processes the 5′ leader sequence of precursor tRNA. Rpp29, a conserved protein subunit of human RNase P, can substitute for C5 protein in reconstitution assays of M1 RNA activity. To better understand the role of the former protein, we compare the mode of action of Rpp29 to that of the C5 protein in activation of M1 RNA. Enzyme kinetic analyses reveal that complexes of M1 RNA–Rpp29 and M1 RNA–C5 exhibit comparable binding affinities to precursor tRNA but different catalytic efficiencies. High concentrations of substrate impede the activity of the former complex. Rpp29 itself exhibits high affinity in substrate binding, which seems to reduce the catalytic efficiency of the reconstituted ribonucleoprotein. Rpp29 has a conserved C-terminal domain with an Sm-like fold that mediates interaction with M1 RNA and precursor tRNA and can activate M1 RNA. The results suggest that distinct protein folds in two unrelated protein cofactors can facilitate transition from RNA- to ribonucleoprotein-based catalysis by RNase P.
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Affiliation(s)
| | | | | | | | - Nayef Jarrous
- To whom correspondence should be addressed. Tel: +972 2 6758233; Fax: +972 2 6784010;
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265
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Livny J, Fogel MA, Davis BM, Waldor MK. sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res 2005; 33:4096-105. [PMID: 16049021 PMCID: PMC1180744 DOI: 10.1093/nar/gki715] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Small non-coding bacterial RNAs (sRNAs) play important regulatory roles in a variety of cellular processes. Nearly all known sRNAs have been identified in Escherichia coli and most of these are not conserved in the majority of other bacterial species. Many of the E.coli sRNAs were initially predicted through bioinformatic approaches based on their common features, namely that they are encoded between annotated open reading frames and are flanked by predictable transcription signals. Because promoter consensus sequences are undetermined for most species, the successful use of bioinformatics to identify sRNAs in bacteria other than E.coli has been limited. We have created a program, sRNAPredict, which uses coordinate-based algorithms to integrate the respective positions of individual predictive features of sRNAs and rapidly identify putative intergenic sRNAs. Relying only on sequence conservation and predicted Rho-independent terminators, sRNAPredict was used to search for sRNAs in Vibrio cholerae. This search identified 9 of the 10 known or putative V.cholerae sRNAs and 32 candidates for novel sRNAs. Small transcripts for 6 out of 9 candidate sRNAs were observed by Northern analysis. Our findings suggest that sRNAPredict can be used to efficiently identify novel sRNAs even in bacteria for which promoter consensus sequences are not available.
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Affiliation(s)
- Jonathan Livny
- To whom correspondence should be addressed. Tel: +1 617 636 2778; Fax: +1 617 636 2723;
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266
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Barik S. Silence of the transcripts: RNA interference in medicine. J Mol Med (Berl) 2005; 83:764-73. [PMID: 16028076 DOI: 10.1007/s00109-005-0690-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Accepted: 05/31/2005] [Indexed: 12/11/2022]
Abstract
Silencing of gene expression by ribonucleic acid (RNA), known as RNA interference (RNAi), is now recognized as a major means of gene regulation in biology. In this mechanism, small noncoding double-stranded RNA molecules knock down gene expression through a variety of mechanisms that include messenger RNA (mRNA) degradation, inhibition of mRNA translation, or chromatin remodeling. The posttranscriptional mechanism of RNAi has been embraced by researchers as a powerful tool for generating deficient phenotypes without mutating the gene. In parallel, exciting recent results have promised its application in disease therapy. This review aims to summarize the current knowledge in this area and provide a roadmap that may eventually launch RNAi from the research bench to the medicine chest.
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Affiliation(s)
- Sailen Barik
- Department of Biochemistry and Molecular Biology, College of Medicine, MSB2370, University of South Alabama, Mobile, 36688-0002, USA.
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267
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Gong H, Liu C, Liu D, Liang C. The role of small RNAs in human diseases: potential troublemaker and therapeutic tools. Med Res Rev 2005; 25:361-81. [PMID: 15637700 PMCID: PMC7168392 DOI: 10.1002/med.20023] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Small RNAs, including short interfering RNAs (siRNAs) and microRNAs (miRNAs), are ubiquitous, versatile repressors of gene expression in plants, animals, and many fungi. They can trigger destruction of homologous mRNA or inhibition of cognate mRNA translation and play an important role in maintaining the stable state of chromosome structure and regulating the expression of protein-coding genes. Furthermore, the recent research showed that there exists close relationship between small RNAs and human diseases. Several human diseases have surfaced in which miRNAs or their machinery might be implicated, such as some neurological diseases and cancers. The specificity and potency of small RNAs suggest that they might be promising as therapeutic agents. This article will review the role of small RNAs in some human diseases etiology and investigations of taking siRNAs as therapeutic tools for treating viral infection, cancer, and other diseases. We also discuss the potential of miRNAs in gene therapy.
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Affiliation(s)
- Huan Gong
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), 5 Dong Dan San Tiao, Beijing 100005, China
| | - Chang‐Mei Liu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), 5 Dong Dan San Tiao, Beijing 100005, China
| | - De‐Pei Liu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), 5 Dong Dan San Tiao, Beijing 100005, China
| | - Chih‐Chuan Liang
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), 5 Dong Dan San Tiao, Beijing 100005, China
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268
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Cho YS, Iguchi N, Yang J, Handel MA, Hecht NB. Meiotic messenger RNA and noncoding RNA targets of the RNA-binding protein Translin (TSN) in mouse testis. Biol Reprod 2005; 73:840-7. [PMID: 15987823 DOI: 10.1095/biolreprod.105.042788] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In postmeiotic male germ cells, TSN, formerly known as testis brain-RNA binding protein, is found in the cytoplasm and functions as a posttranscriptional regulator of a group of genes transcribed by the transcription factor CREM-tau. In contrast, in pachytene spermatocytes, TSN is found predominantly in nuclei. Tsn-null males show a reduced sperm count and high levels of apoptosis in meiotic cells, suggesting a critical function for TSN during meiosis. To identify meiotic target RNAs that associate in vivo with TSN, we reversibly cross-linked TSN to RNA in testis extracts from 17-day-old and adult mice and immunoprecipitated the complexes with an affinity-purified TSN antibody. Extracts from Tsn-null mice were used as controls. Cloning and sequencing the immunoprecipitated RNAs, we identified four new TSN target mRNAs, encoding diazepam-binding inhibitor-like 5, arylsulfatase A, a tetratricopeptide repeat structure-containing protein, and ring finger protein 139. In contrast to the population of postmeiotic translationally delayed mRNAs that bind TSN, these four mRNAs are initially expressed in pachytene spermatocytes. In addition, anti-TSN also precipitated a nonprotein-coding RNA (ncRNA), which is abundant in nuclei of pachytene spermatocytes and has a putative polyadenylation signal, but no open reading frame. A second similar ncRNA is adjacent to a GGA repeat, a motif frequently associated with recombination hot spots. RNA gel-shift assays confirm that the four new target mRNAs and the ncRNA specifically bind to TSN in testis extracts. These studies have, for the first time, identified both mRNAs and a ncRNA as TSN targets expressed during meiosis.
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Affiliation(s)
- Yoon Shin Cho
- Center for Research on Reproduction and Women's Health, University of Pennsylvania School of Medicine, Philadelphia, 19104, USA
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269
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Havilio M, Levanon EY, Lerman G, Kupiec M, Eisenberg E. Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome. BMC Genomics 2005; 6:93. [PMID: 15960846 PMCID: PMC1181813 DOI: 10.1186/1471-2164-6-93] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Accepted: 06/16/2005] [Indexed: 11/23/2022] Open
Abstract
Background Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae. Results Taking into account the absence of a significantly large yeast EST database, we use microarray expression data collected for genomic regions erroneously believed to be coding to study the expression pattern of non-coding regions in the Saccharomyces cerevisiae genome. We find that at least 164 out of 589 (28%) such regions are expressed under specific biological conditions. In particular, looking at the probes that are located opposing other known genes at the same genomic locus, we find that 88 out of 341 (26%) of these genes support antisense transcription. The expression patterns of these antisense genes are positively correlated. We validate these results using RT-PCR on a sample of 6 non-coding transcripts. Conclusion 1. The yeast genome is transcribed on a scale larger than previously assumed. 2. Correlated transcription of antisense genes is abundant in the yeast genome. 3. Antisense genes in yeast are non-coding.
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Affiliation(s)
- Moshe Havilio
- Compugen Ltd., 72 Pinchas Rosen St., Tel-Aviv 69512, Israel
| | - Erez Y Levanon
- Compugen Ltd., 72 Pinchas Rosen St., Tel-Aviv 69512, Israel
- Department of Pediatric Hematology-Oncology, Chaim Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Galia Lerman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Eli Eisenberg
- Compugen Ltd., 72 Pinchas Rosen St., Tel-Aviv 69512, Israel
- School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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270
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Borukhov S, Lee J, Laptenko O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol Microbiol 2005; 55:1315-24. [PMID: 15720542 DOI: 10.1111/j.1365-2958.2004.04481.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Like transcription initiation, the elongation and termination stages of transcription cycle serve as important targets for regulatory factors in prokaryotic cells. In this review, we discuss the recent progress in structural and biochemical studies of three evolutionarily conserved elongation factors, GreA, NusA and Mfd. These factors affect RNA polymerase (RNAP) processivity by modulating transcription pausing, arrest, termination or anti-termination. With structural information now available for RNAP and models of ternary elongation complexes, the interaction between these factors and RNAP can be modelled, and possible molecular mechanisms of their action can be inferred. The models suggest that these factors interact with RNAP at or near its three major, nucleic acid-binding channels: Mfd near the upstream opening of the primary (DNA-binding) channel, NusA in the vicinity of both the primary channel and the RNA exit channel, and GreA within the secondary (backtracked RNA-binding) channel, and support the view that these channels are involved in the maintenance of RNAP processivity.
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Affiliation(s)
- Sergei Borukhov
- Department of Microbiology and Immunology, SUNY Health Sciences Center at Brooklyn, Brooklyn, NY 11203, USA.
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271
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Saetrom P, Sneve R, Kristiansen KI, Snøve O, Grünfeld T, Rognes T, Seeberg E. Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. Nucleic Acids Res 2005; 33:3263-70. [PMID: 15942029 PMCID: PMC1143698 DOI: 10.1093/nar/gki644] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Several methods exist for predicting non-coding RNA (ncRNA) genes in Escherichia coli (E.coli). In addition to about sixty known ncRNA genes excluding tRNAs and rRNAs, various methods have predicted more than thousand ncRNA genes, but only 95 of these candidates were confirmed by more than one study. Here, we introduce a new method that uses automatic discovery of sequence patterns to predict ncRNA genes. The method predicts 135 novel candidates. In addition, the method predicts 152 genes that overlap with predictions in the literature. We test sixteen predictions experimentally, and show that twelve of these are actual ncRNA transcripts. Six of the twelve verified candidates were novel predictions. The relatively high confirmation rate indicates that many of the untested novel predictions are also ncRNAs, and we therefore speculate that E.coli contains more ncRNA genes than previously estimated.
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Affiliation(s)
- Pål Saetrom
- Interagon AS, Medisinsk teknisk senter NO-7489 Trondheim, Norway.
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272
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Mansilla F, Hansen LL, Jakobsen H, Kjeldgaard NO, Clark BFC, Knudsen CR. Deconstructing PTI-1: PTI-1 is a truncated, but not mutated, form of translation elongatin factor 1A1, eEF1A1. ACTA ACUST UNITED AC 2005; 1727:116-24. [PMID: 15716006 DOI: 10.1016/j.bbaexp.2004.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Revised: 12/15/2004] [Accepted: 12/16/2004] [Indexed: 11/30/2022]
Abstract
The prostate tumor-inducing gene 1 (PTI-1) transcript is detected in various human carcinoma cells. PTI-1 is reported to consist of a 5' untranslated region (5' UTR) homologous to mycoplasma 23S rRNA and a coding region corresponding to a truncated and mutated form of the translation elongation factor 1A, eEF1A. We have found that the PTI-1 transcript may encode a truncated, but not mutated, form of the human isoform eEF1A1. Additionally, the 5' UTR sequence of PTI-1 from genomic DNA of different cell lines and blood samples varies from the original sequence. This 5' -UTR region of PTI-1 presents a fusion of E. coli and Mycoplasma hyorhinis 23S rRNA. We have overexpressed the potential PTI-1 protein in E. coli and various human cell lines. The resulting protein could be detected by western blotting using anti-eEF1A antibodies. However, we were unable to detect the PTI-1 protein in LNCaP cell extracts. The potential roles of the PTI-1 protein in carcinogenesis and the origin of the PTI-1 gene in the human genome are discussed.
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Affiliation(s)
- Francisco Mansilla
- Department of Molecular Biology, University of Aarhus, Arhus C, Denmark.
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273
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Vizirianakis IS, Tsiftsoglou AS. Blockade of murine erythroleukemia cell differentiation by hypomethylating agents causes accumulation of discrete small poly(A)- RNAs hybridized to 3'-end flanking sequences of beta(major) globin gene. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1743:101-14. [PMID: 15777845 DOI: 10.1016/j.bbamcr.2004.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 09/02/2004] [Accepted: 09/03/2004] [Indexed: 11/26/2022]
Abstract
Induction of murine erythroleukemia (MEL) cell differentiation is accompanied by transcriptional activation of globin genes and biosynthesis of hemoglobin. In this study, we observed cytoplasmic accumulation of relatively small RNAs of different size (150-600 nt) hybridized to alpha1 and beta(major) globin DNA probes in MEL cells blocked to differentiate by hypomethylating agents (neplanocin A, 3-deazaneplanocin A and cycloleucine). These RNAs lack poly(A) tail and appear to be quite stable. Search within the 3'-end flanking sequences of beta(major) globin gene revealed the presence of a B1 repeat element, several ATG initiation codons, a GATA-1 consensus sequence and sequences recognized by AP-1/NF-E2 and erythroid Krüppel-like factor (EKLF) transcription factors. These data taken together indicate that exposure of MEL cells to hypomethylating agents promotes accumulation of relatively small discrete RNA transcripts lacking poly(A) tail regardless of the presence or absence of inducer dimethylsulfoxide (DMSO). However, the relative steady-state level of small RNAs was comparatively higher in cells co-exposed to inducer and each one of the hypomethylating agents. Although the orientation of these RNAs has not been established as yet, the possibility these small poly(A)- RNAs which are induced by hypomethylating agents may be involved in the blockade of MEL cell differentiation program is discussed.
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Affiliation(s)
- Ioannis S Vizirianakis
- Laboratory of Pharmacology, Department of Pharmaceutical Sciences, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece.
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274
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Liu C, Bai B, Skogerbø G, Cai L, Deng W, Zhang Y, Bu D, Zhao Y, Chen R. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 2005; 33:D112-5. [PMID: 15608158 PMCID: PMC539995 DOI: 10.1093/nar/gki041] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of ncRNAs, except transfer RNAs and ribosomal RNAs. (ii) All ncRNA sequences and their related information (e.g. function, cellular role, cellular location, chromosomal information, etc.) in NONCODE have been confirmed manually by consulting relevant literature: more than 80% of the entries are based on experimental data. (iii) Based on the cellular process and function, which a given ncRNA is involved in, we introduced a novel classification system, labeled process function class, to integrate existing classification systems. (iv) In addition, some 1100 ncRNAs have been grouped into nine other classes according to whether they are specific to gender or tissue or associated with tumors and diseases, etc. (v) NONCODE provides a user-friendly interface, a visualization platform and a convenient search option, allowing efficient recovery of sequence, regulatory elements in the flanking sequences, secondary structure, related publications and other information. The first release of NONCODE (v1.0) contains 5339 non-redundant sequences from 861 organisms, including eukaryotes, eubacteria, archaebacteria, virus and viroids. Access is free for all users through a web interface at http://noncode.bioinfo.org.cn.
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Affiliation(s)
- Changning Liu
- Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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275
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Biro JC. Seven fundamental, unsolved questions in molecular biology. Cooperative storage and bi-directional transfer of biological information by nucleic acids and proteins: an alternative to "central dogma". Med Hypotheses 2005; 63:951-62. [PMID: 15504561 DOI: 10.1016/j.mehy.2004.06.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2004] [Accepted: 06/14/2004] [Indexed: 11/24/2022]
Abstract
The Human Genome Mapping Project provided us a large amount of sequence data. However our understanding of these data did not grow proportionally, because old dogmas still set the limits of our thinking. The gene-centric, reductionistical side of molecular biology is reviewed and seven problems are formulated, each indicating the insufficiency of the "central dogma". The following is concluded and suggested: 1. Genes are located and expressed on both DNA strands; 2. Introns are the source of important biological regulation and diversity; 3. Repeats are the frame of the chromatin structure and participate in the chromatin regulation; 4. The molecular accessibility of the canonical dsDNA structure is poor; 5. The genetic code is co-evolved with the amino acids and there is a stereochemical matching between the codes andamino acids; 6. The flow of information between nucleic acids and proteins is bi-directional and reverse translation might exist; 7. Complex genetic information is always carried and stored by nucleic acids and proteins together.
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Affiliation(s)
- J C Biro
- Karolinska Institute, Stockholm, Sweden.
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276
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Argani P, Laé M, Hutchinson B, Reuter VE, Collins MH, Perentesis J, Tomaszewski JE, Brooks JSJ, Acs G, Bridge JA, Vargas SO, Davis IJ, Fisher DE, Ladanyi M. Renal carcinomas with the t(6;11)(p21;q12): clinicopathologic features and demonstration of the specific alpha-TFEB gene fusion by immunohistochemistry, RT-PCR, and DNA PCR. Am J Surg Pathol 2005; 29:230-40. [PMID: 15644781 DOI: 10.1097/01.pas.0000146007.54092.37] [Citation(s) in RCA: 202] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A highly distinctive subset of renal neoplasms of children and young adults contains a t(6;11)(p21;q12), a translocation recently been shown to result in fusion of Alpha, a gene on 11q12, with the transcription factor gene TFEB on 6p21. To define the clinicopathologic spectrum of this nascent entity and to establish immunohistochemical (IHC) and molecular methods for the detection of the specific Alpha-TFEB fusion, we studied 7 renal neoplasms that showed the t(6;11) by cytogenetic or molecular analysis (patient age: range, 9-33 years; mean, 17 years). While all tumors were confined to the kidney, 3 tumors demonstrated vascular invasion. In limited follow-up, none has metastasized. We postulated that the Alpha-TFEB gene fusion may result in deregulated expression of TFEB protein that would be detectable by IHC. Using a polyclonal antibody to TFEB on formalin-fixed, paraffin-embedded tissue sections, we found that all 7 renal neoplasms with the t(6;11) demonstrated moderate (2 cases) or strong (5 cases) nuclear TFEB immunoreactivity. In contrast, none of 1089 other tumors (of 74 histologic types from 16 sites) labeled significantly for TFEB. Nuclear immunoreactivity for TFEB in normal tissues was extremely rare, limited to weak labeling of scattered benign lymphocytes. We also show that the Alpha-TFEB fusion RNAs are highly variable in size and structure, making detection by reverse-transcriptase polymerase chain reaction (RT-PCR) less reliable than for other gene fusions. Because Alpha is an intronless gene and therefore lacks splice signals, we hypothesized that DNA PCR and RT-PCR products would be identical, allowing for the use of more robust molecular assays based on genomic DNA. Indeed, in 2 cases with available frozen tissue, we showed the genomic Alpha-TFEB junction detected by DNA PCR to be identical to the Alpha-TFEB fusion mRNA detected by RT-PCR. In summary, renal neoplasms with the t(6;11) are a distinctive neoplastic entity with many similarities to the Xp11 translocation carcinomas, and together with the latter form a growing "MiTF/TFE family" of translocation carcinomas. Nuclear immunoreactivity for TFEB protein is a highly sensitive and specific diagnostic marker for these renal neoplasms. Finally, the special molecular features of the Alpha-TFEB gene fusion allow its molecular detection by DNA PCR as a robust alternative to RT-PCR in clinical tumor samples.
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Affiliation(s)
- Pedram Argani
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
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277
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Pasquali S, Gan HH, Schlick T. Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nucleic Acids Res 2005; 33:1384-98. [PMID: 15745998 PMCID: PMC552955 DOI: 10.1093/nar/gki267] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Modular architecture is a hallmark of RNA structures, implying structural, and possibly functional, similarity among existing RNAs. To systematically delineate the existence of smaller topologies within larger structures, we develop and apply an efficient RNA secondary structure comparison algorithm using a newly developed two-dimensional RNA graphical representation. Our survey of similarity among 14 pseudoknots and subtopologies within ribosomal RNAs (rRNAs) uncovers eight pairs of structurally related pseudoknots with non-random sequence matches and reveals modular units in rRNAs. Significantly, three structurally related pseudoknot pairs have functional similarities not previously known: one pair involves the 3′ end of brome mosaic virus genomic RNA (PKB134) and the alternative hammerhead ribozyme pseudoknot (PKB173), both of which are replicase templates for viral RNA replication; the second pair involves structural elements for translation initiation and ribosome recruitment found in the viral internal ribosome entry site (PKB223) and the V4 domain of 18S rRNA (PKB205); the third pair involves 18S rRNA (PKB205) and viral tRNA-like pseudoknot (PKB134), which probably recruits ribosomes via structural mimicry and base complementarity. Additionally, we quantify the modularity of 16S and 23S rRNAs by showing that RNA motifs can be constructed from at least 210 building blocks. Interestingly, we find that the 5S rRNA and two tree modules within 16S and 23S rRNAs have similar topologies and tertiary shapes. These modules can be applied to design novel RNA motifs via build-up-like procedures for constructing sequences and folds.
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Affiliation(s)
| | - Hin Hark Gan
- Department of Chemistry, New York University251 Mercer Street, New York, NY 10021, USA
| | - Tamar Schlick
- Department of Chemistry, New York University251 Mercer Street, New York, NY 10021, USA
- Courant Institute of Mathematical Sciences, New York University251 Mercer Street, New York, NY 10021, USA
- To whom correspondence should be addressed: Tel: +1 212 998 3116; Fax: +1 212 995 4152;
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278
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Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 2005; 102:2454-9. [PMID: 15665081 PMCID: PMC548974 DOI: 10.1073/pnas.0409169102] [Citation(s) in RCA: 520] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Indexed: 01/22/2023] Open
Abstract
We report an efficient method for detecting functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, already has yielded excellent results for a small number of aligned sequences and is suitable for large-scale genomic screens. It consists of two basic components: (i) a measure for RNA secondary structure conservation based on computing a consensus secondary structure, and (ii) a measure for thermodynamic stability, which, in the spirit of a z score, is normalized with respect to both sequence length and base composition but can be calculated without sampling from shuffled sequences. Functional RNA secondary structures can be identified in multiple sequence alignments with high sensitivity and high specificity. We demonstrate that this approach is not only much more accurate than previous methods but also significantly faster. The method is implemented in the program rnaz, which can be downloaded from www.tbi.univie.ac.at/~wash/RNAz. We screened all alignments of length n > or = 50 in the Comparative Regulatory Genomics database, which compiles conserved noncoding elements in upstream regions of orthologous genes from human, mouse, rat, Fugu, and zebrafish. We recovered all of the known noncoding RNAs and cis-acting elements with high significance and found compelling evidence for many other conserved RNA secondary structures not described so far to our knowledge.
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Affiliation(s)
- Stefan Washietl
- Department of Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria
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279
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Buskirk AR, Landrigan A, Liu DR. Engineering a ligand-dependent RNA transcriptional activator. ACTA ACUST UNITED AC 2005; 11:1157-63. [PMID: 15324817 DOI: 10.1016/j.chembiol.2004.05.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Revised: 05/21/2004] [Accepted: 05/25/2004] [Indexed: 01/12/2023]
Abstract
RNA has recently been shown to play diverse roles in gene regulation, including the small molecule-dependent inhibition of translation in prokaryotes. To create an artificial genetic switch that acts at the level of transcription, we fused a small molecule binding aptamer to a previously evolved RNA that activates transcription when localized to a promoter. We designed a conformational shift in which a helical element required for transcriptional activation was stabilized upon ligand binding. Selection and screening in S. cerevisiae optimized the linker region, generating an RNA that is 10-fold more active in the presence of tetramethylrosamine (TMR). TMR increases the activity of this evolved RNA in a graded, dose-dependent manner. Our results exemplify a strategy for controlling the activity of laboratory-evolved RNAs in living cells.
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Affiliation(s)
- Allen R Buskirk
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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280
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Affiliation(s)
- Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
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281
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Lease RA, Woodson SA. Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J Mol Biol 2005; 344:1211-23. [PMID: 15561140 DOI: 10.1016/j.jmb.2004.10.006] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 09/22/2004] [Accepted: 10/06/2004] [Indexed: 11/15/2022]
Abstract
Small RNAs (sRNAs) regulate bacterial genes involved in environmental adaptation. This RNA regulation requires Hfq, a bacterial Sm-like protein that stabilizes sRNAs and enhances RNA-RNA interactions. To understand the mechanism of target recognition by sRNAs, we investigated the interactions between Hfq, the sRNA DsrA, and its regulatory target rpoS mRNA, which encodes the stress response sigma factor. Nuclease footprinting revealed that Hfq recognized multiple sites in rpoS mRNA without significantly perturbing secondary structure in the 5' leader that inhibits translation initiation. Base-pairing with DsrA, however, made the rpoS ribosome binding site fully accessible, as predicted by genetic data. Hfq bound DsrA four times more tightly than the DsrA.rpoS RNA complex in gel mobility-shift assays. Consequently, Hfq is displaced rapidly from its high-affinity binding site on DsrA by conformational changes in DsrA, when DsrA base-pairs with rpoS mRNA. Hfq accelerated DsrA.rpoS RNA association and stabilized the RNA complex up to twofold. Hybridization of DsrA and rpoS mRNA was optimal when Hfq occupied its primary binding site on free DsrA, but was inhibited when Hfq associated with the DsrA.rpoS RNA complex. We conclude that recognition of rpoS mRNA is stimulated by binding of Hfq to free DsrA sRNA, followed by release of Hfq from the sRNA.mRNA complex.
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Affiliation(s)
- Richard A Lease
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218-2865, USA
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282
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Profiling and Searching for RNA Pseudoknot Structures in Genomes. TRANSACTIONS ON COMPUTATIONAL SYSTEMS BIOLOGY II 2005. [PMCID: PMC7120494 DOI: 10.1007/11567752_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for structures that contain pseudoknot in genomes of a variety of organisms.
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283
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284
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Abstract
Small noncoding RNAs have been found in all organisms, primarily as regulators of translation and message stability. The most exhaustive searches have taken place in E. coli, resulting in identification of more than 50 small RNAs, or 1%-2% of the number of protein-coding genes. One large class of these small RNAs uses the RNA chaperone Hfq; members of this class act by pairing to target messenger RNAs. Among the members of this class are DsrA and RprA, which positively regulate rpoS translation, OxyS, which negatively regulates rpoS translation and fhlA translation, RyhB, which reapportions iron use in the cell by downregulating translation of many genes that encode Fe-containing proteins, and Spot 42, which changes the polarity of translation in the gal operon. The promoters of these small RNAs are tightly regulated, frequently as part of well-understood regulons. Lessons learned from the study of small RNAs in E. coli can be applied to finding these important regulators in other organisms.
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA.
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285
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Wyszyńska-Koko J, Kurył J. Porcine MYF6 gene: sequence, homology analysis, and variation in the promoter region. Anim Biotechnol 2004; 15:159-73. [PMID: 15595701 DOI: 10.1081/labt-200038667] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
MYF6 gene codes for the bHLH transcription factor belonging to MyoD family. Its expression accompanies the processes of differentiation and maturation of myotubes during embriogenesis and continues on a relatively high level after birth, affecting the muscle phenotype. The porcine MYF6 gene was amplified and sequenced and compared with MYF6 gene sequences of other species. The amino acid sequence was deduced and an interspecies homology analysis was performed. Myf-6 protein shows a high conservation among species of 99 and 97% identity when comparing pig with cow and human, respectively, and of 93% when comparing pig with mouse and rat. The single nucleotide polymorphism (SNP) was revealed within the promoter region, which appeared to be T --> C transition recognized by a MspI restriction enzyme.
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Affiliation(s)
- J Wyszyńska-Koko
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, Wolka Kosowska, Poland.
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286
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Abstract
RNA is structurally very flexible, which provides the basis for its functional diversity. An RNA molecule can often adopt different conformations, which enables the regulation of its function through folding. Proteins help RNAs reach their functionally active conformation by increasing their structural stability or by chaperoning the folding process. Large, dynamic RNA-protein complexes, such as the ribosome or the spliceosome, require numerous proteins that coordinate conformational switches of the RNA components during assembly and during their respective activities.
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Affiliation(s)
- Renée Schroeder
- Max F. Perutz Laboratories, Department of Microbiology and Genetics, University of Vienna, Austria.
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287
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Wahl MB, Heinzmann U, Imai K. LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome. Bioinformatics 2004; 21:1389-92. [PMID: 15585522 DOI: 10.1093/bioinformatics/bti205] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Despite the increasing notions of the functional importance of antisense transcripts in gene regulation, the genome-wide overview on the ontology of antisense genes has not been obtained. Therefore, we tried to find novel antisense genes genome-wide by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS We identified 1260 potential antisense genes, of which 1001 are not annotated in EnsEMBL, thereby being regarded as novel. Interestingly their sense counterparts were co-expressed in the majority of the cases. CONCLUSIONS The use of LongSAGE transcriptome data is extremely powerful in the identification of thus-far unknown antisense transcripts, even in the case of well-characterized organisms like the mouse. CONTACT imai@gsf.de.
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Affiliation(s)
- Matthias B Wahl
- Institute of Developmental Genetics, GSF-National Research Center for Environment and Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
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288
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Abstract
Immediate-early viral gene products of human cytomegalovirus (HCMV) are derived from several genomic loci and largely serve to establish a cellular environment conducive to viral replication. We have further examined an unusual immediate-early transcript known as the 5-kb RNA, concluding that it is a stable intron encoded by HCMV. The 5-kb RNA is highly AT rich in sequence and lacks open reading frames likely to be translated into protein. We confirmed the absence of polyadenylation of the transcript and showed that it is primarily nuclear localized during viral infection. We mapped the 5' end of the 5-kb RNA to a consensus splice donor site and localized the 3' end in the vicinity of a splice acceptor site. In transfection studies, we showed that the 5-kb RNA can be spliced from a heterologous primary transcript. Using bacterial artificial chromosome technology, we constructed a viral recombinant containing a mutation in the 5' splice donor site that defines the 5' end of the RNA and found that this mutation eliminates expression of the 5-kb RNA during viral infection. This mutant grows in human fibroblasts without complementation. Taken together, these data support the conclusion that the 5-kb RNA is a stable intron expressed by HCMV.
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Affiliation(s)
- Caroline A Kulesza
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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289
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Finishing the euchromatic sequence of the human genome. Nature 2004; 431:931-45. [PMID: 15496913 DOI: 10.1038/nature03001] [Citation(s) in RCA: 2806] [Impact Index Per Article: 140.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Accepted: 09/07/2004] [Indexed: 12/13/2022]
Abstract
The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers approximately 99% of the euchromatic genome and is accurate to an error rate of approximately 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.
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290
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Mikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, Feig AL. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat Struct Mol Biol 2004; 11:1206-14. [PMID: 15531892 PMCID: PMC3071270 DOI: 10.1038/nsmb858] [Citation(s) in RCA: 212] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 09/30/2004] [Indexed: 11/08/2022]
Abstract
The bacterial Sm-like protein Hfq facilitates RNA-RNA interactions involved in post-transcriptional regulation of the stress response. Specifically, Hfq helps pair noncoding RNAs (ncRNAs) with complementary regions of target mRNAs. To probe the mechanism of this pairing, we generated a series of Hfq mutants and measured their affinity for RNAs like those with which Hfq must associate in vivo. We tested the mutants' DsrA-dependent activation of rpoS, and their ability to stabilize DsrA ncRNA against degradation in vivo. Our results suggest that Hfq has two independent RNA-binding surfaces. In addition to a well-known site around the core of the Hfq hexamer, we observe interactions with the distal face of Hfq, a new locus with which mRNAs and poly(A) sequences associate. Our model explains how Hfq can simultaneously bind a ncRNA and its mRNA target to facilitate the strand displacement reaction required for Hfq-dependent translational regulation.
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Affiliation(s)
- Peter J Mikulecky
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, USA
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291
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Abstract
The recent discoveries of RNA interference and related RNA silencing pathways have revolutionized our understanding of gene regulation. RNA interference has been used as a research tool to control the expression of specific genes in numerous experimental organisms and has potential as a therapeutic strategy to reduce the expression of problem genes. At the heart of RNA interference lies a remarkable RNA processing mechanism that is now known to underlie many distinct biological phenomena.
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Affiliation(s)
- Craig C Mello
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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292
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Kim N, Shiffeldrim N, Gan HH, Schlick T. Candidates for novel RNA topologies. J Mol Biol 2004; 341:1129-44. [PMID: 15321711 DOI: 10.1016/j.jmb.2004.06.054] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Revised: 06/10/2004] [Accepted: 06/21/2004] [Indexed: 10/26/2022]
Abstract
Because the functional repertiore of RNA molecules, like proteins, is closely linked to the diversity of their shapes, uncovering RNA's structural repertoire is vital for identifying novel RNAs, especially in genomic sequences. To help expand the limited number of known RNA families, we use graphical representation and clustering analysis of RNA secondary structures to predict novel RNA topologies and their abundance as a function of size. Representing the essential topological properties of RNA secondary structures as graphs enables enumeration, generation, and prediction of novel RNA motifs. We apply a probabilistic graph-growing method to construct the RNA structure space encompassing the topologies of existing and hypothetical RNAs and cluster all RNA topologies into two groups using topological descriptors and a standard clustering algorithm. Significantly, we find that nearly all existing RNAs fall into one group, which we refer to as "RNA-like"; we consider the other group "non-RNA-like". Our method predicts many candidates for novel RNA secondary topologies, some of which are remarkably similar to existing structures; interestingly, the centroid of the RNA-like group is the tmRNA fold, a pseudoknot having both tRNA-like and mRNA-like functions. Additionally, our approach allows estimation of the relative abundance of pseudoknot and other (e.g. tree) motifs using the "edge-cut" property of RNA graphs. This analysis suggests that pseudoknots dominate the RNA structure universe, representing more than 90% when the sequence length exceeds 120 nt; the predicted trend for <100 nt agrees with data for existing RNAs. Together with our predictions for novel "RNA-like" topologies, our analysis can help direct the design of functional RNAs and identification of novel RNA folds in genomes through an efficient topology-directed search, which grows much more slowly in complexity with RNA size compared to the traditional sequence-based search.
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Affiliation(s)
- Namhee Kim
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
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293
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Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res 2004; 32:4925-36. [PMID: 15448187 PMCID: PMC519121 DOI: 10.1093/nar/gkh839] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences, e.g. compact viral genomes, can simultaneously encode functional RNA structures as well as proteins, and evidence is accumulating that this phenomenon may also be found in Eukaryotes. We here present the first comparative method, called RNA-DECODER, which explicitly takes the known protein-coding context of an RNA-sequence alignment into account in order to predict evolutionarily conserved secondary-structure elements, which may span both coding and non-coding regions. RNA-DECODER employs a stochastic context-free grammar together with a set of carefully devised phylogenetic substitution-models, which can disentangle and evaluate the different kinds of overlapping evolutionary constraints which arise. We show that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD.
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Affiliation(s)
- Jakob Skou Pedersen
- Bioinformatics Research Center, Department of Ecology and Genetics, The Institute of Biological Sciences, University of Aarhus, Ny Munkegade, Building 550, 8000 Aarhus C, Denmark.
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294
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Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker DD. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol 2004; 5:R73. [PMID: 15461792 PMCID: PMC545593 DOI: 10.1186/gb-2004-5-10-r73] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 07/07/2004] [Accepted: 08/16/2004] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from approximately 50,000 known and predicted transcript sequences from the human genome were used to survey transcription from a diverse set of 60 tissues and cell lines using ink-jet microarrays. Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22. RESULTS The combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts. This set of high-confidence transcripts represents the first experimentally driven annotation of the human genome. In addition, the results from genomic tiling suggest that a large amount of transcription exists outside of annotated regions of the genome and serves as an example of how this activity could be measured on a genome-wide scale. CONCLUSIONS These data represent one of the most comprehensive assessments of transcriptional activity in the human genome and provide an atlas of human gene expression over a unique set of gene predictions. Before the annotation of the human genome is considered complete, however, the previously unannotated transcriptional activity throughout the genome must be fully characterized.
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Affiliation(s)
- Eric E Schadt
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Stephen W Edwards
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | | | - Dan Holder
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Lisa Ying
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Vladimir Svetnik
- Merck Research Laboratories, W42-213 Sumneytown Pike, POB 4, Westpoint, PA 19846, USA
| | - Amy Leonardson
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Kyle W Hart
- Rally Scientific, 41 Fayette Street, Suite 1, Watertown, MA 02472, USA
| | - Archie Russell
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Guoya Li
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Guy Cavet
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - John Castle
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Paul McDonagh
- Amgen Inc, 1201 Amgen Court W, Seattle, WA 98119, USA
| | - Zhengyan Kan
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Ronghua Chen
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Andrew Kasarskis
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Mihai Margarint
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Ramon M Caceres
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | - Jason M Johnson
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
| | | | | | | | - Daniel D Shoemaker
- Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
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295
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Starostina NG, Marshburn S, Johnson LS, Eddy SR, Terns RM, Terns MP. Circular box C/D RNAs in Pyrococcus furiosus. Proc Natl Acad Sci U S A 2004; 101:14097-101. [PMID: 15375211 PMCID: PMC521125 DOI: 10.1073/pnas.0403520101] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Box C/D RNAs are small, noncoding RNAs that function in RNA modification in eukaryotes and archaea. Here, we report that box C/D RNAs exist in the rare biological form of RNA circles in the hyperthermophilic archaeon Pyrococcus furiosus. Northern analysis of box C/D RNAs reveals two prominent RNA species of different electrophoretic mobilities in total P. furiosus RNA preparations. Together, the results of Northern, ribozyme, RT-PCR, and lariat debranching analyses indicate that the two species are circular and linear RNAs of similar length and abundance. It seems that most, if not all, species of box C/D RNAs exist as circles in P. furiosus. In addition, the circular RNAs are found in complexes with proteins required for box C/D RNA function. Our finding places box C/D RNAs among the extremely few circular RNAs known to exist in nature. Moreover, the unexpected discovery of circular box C/D RNAs points to the existence of a previously unrecognized biogenesis pathway for box C/D RNAs in archaea.
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MESH Headings
- Animals
- Base Sequence
- Blotting, Northern
- Blotting, Western
- Conserved Sequence
- Immunoprecipitation/methods
- Molecular Sequence Data
- Nucleic Acid Conformation
- Pyrococcus furiosus/chemistry
- Pyrococcus furiosus/genetics
- RNA/genetics
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Catalytic/analysis
- RNA, Catalytic/genetics
- RNA, Circular
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- Rabbits
- Recombinant Proteins/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins, Small Nucleolar/genetics
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Affiliation(s)
- Natalia G Starostina
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Science Building, Athens, GA 30602, USA
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296
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Suzuki M, Hayashizaki Y. Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. Bioessays 2004; 26:833-43. [PMID: 15273986 DOI: 10.1002/bies.20084] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The largest transcriptome reported so far comprises 60,770 mouse full-length cDNA clones, and is an effective reference data set for comparative transcriptomics. The number of mouse cDNAs identified greatly exceeds the number of genes predicted from the sequenced human and mouse genomes. This is largely because of extensive alternative splicing and the presence of many non-coding RNAs (ncRNAs), which are difficult to predict from genomic sequences. Notably, ncRNAs are a major component of the transcriptomes of higher organisms, and many sense-antisense pairs have been identified. The ncRNAs function in a range of regulatory mechanisms for gene expression and other biological processes. They might also have contributed to the increased functional diversification of genomes during evolution. In this review, we discuss aspects of the transcriptome of various organisms in relation to the mouse data, in order to shed light on the regulatory mechanisms and physiological significance of these abundant RNAs.
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Affiliation(s)
- Masanori Suzuki
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan
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297
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Abstract
6S RNA was identified in Escherichia coli >30 years ago, but the physiological role of this RNA has remained elusive. Here, we demonstrate that 6S RNA-deficient cells are at a disadvantage for survival in stationary phase, a time when 6S RNA regulates transcription. Growth defects were most apparent as a decrease in the competitive fitness of cells lacking 6S RNA. To decipher the molecular mechanisms underlying the growth defects, we have expanded studies of 6S RNA effects on transcription. 6S RNA inhibition of sigma(70)-dependent transcription was not ubiquitous, in spite of the fact that the vast majority of sigma(70)-RNA polymerase is bound by 6S RNA during stationary phase. The sigma(70)-dependent promoters inhibited by 6S RNA contain an extended -10 promoter element, suggesting that this feature may define a class of 6S RNA-regulated genes. We also discovered a secondary effect of 6S RNA in the activation of sigma(S)-dependent transcription at several promoters. We conclude that 6S RNA regulation of both sigma(70) and sigma(S) activities contributes to increased cell persistence during nutrient deprivation.
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Affiliation(s)
- Amy E Trotochaud
- Department of Bacteriology, 420 Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA
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298
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Wachi M, Ogawa T, Yokoyama K, Hokii Y, Shimoyama M, Muto A, Ushida C. Isolation of eight novel Caenorhabditis elegans small RNAs. Gene 2004; 335:47-56. [PMID: 15194189 DOI: 10.1016/j.gene.2004.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Revised: 02/23/2004] [Accepted: 03/05/2004] [Indexed: 11/22/2022]
Abstract
Eight novel small RNAs that were encoded in the regions corresponding to the introns of protein-coding genes were isolated from Caenorhabditis elegans. Seven of them showed a typical snoRNA secondary structure: one C/D snoRNA and six H/ACA snoRNAs. The remaining one RNA did not show any homology to other RNAs in a database. Four of the seven isolated snoRNAs could form base pairings with parts of rRNAs, suggesting that they are potential pseudouridilation sites and methylation sites. The results of our study suggest that there are more as-yet-unidentified small ncRNAs of which genes are located in the intron regions of protein-coding genes in C. elegans.
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MESH Headings
- Animals
- Base Sequence
- Caenorhabditis/genetics
- Caenorhabditis elegans/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Genes, Helminth/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Helminth/chemistry
- RNA, Helminth/genetics
- RNA, Helminth/isolation & purification
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/isolation & purification
- Sequence Alignment
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- M Wachi
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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299
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Coventry A, Kleitman DJ, Berger B. MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci U S A 2004; 101:12102-7. [PMID: 15304649 PMCID: PMC514400 DOI: 10.1073/pnas.0404193101] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Indexed: 11/18/2022] Open
Abstract
We present a highly accurate method for identifying genes with conserved RNA secondary structure by searching multiple sequence alignments of a large set of candidate orthologs for correlated arrangements of reverse-complementary regions. This approach is growing increasingly feasible as the genomes of ever more organisms are sequenced. A program called msari implements this method and is significantly more accurate than existing methods in the context of automatically generated alignments, making it particularly applicable to high-throughput scans. In our tests, it discerned clustalw-generated multiple sequence alignments of signal recognition particle or RNaseP orthologs from controls with 89.1% sensitivity at 97.5% specificity and with 74.4% sensitivity with no false positives in 494 controls. We used msari to conduct a comprehensive scan for secondary structure in mRNAs of coding genes, and we found many genes with known mRNA secondary structure and compelling evidence for secondary structure in other genes. msari uses a method for coping with sequence redundancy that is likely to have applications in a large set of other comparison-based search methods. The program is available for download from http://theory.csail.mit.edu/MSARi.
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Affiliation(s)
- Alex Coventry
- Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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300
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Zhou N, Fang J, Mukhtar M, Acheampong E, Pomerantz RJ. Inhibition of HIV-1 fusion with small interfering RNAs targeting the chemokine coreceptor CXCR4. Gene Ther 2004; 11:1703-12. [PMID: 15306840 DOI: 10.1038/sj.gt.3302339] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
RNA interference (RNAi) is an evolutionarily conserved process by which plants and animals protect their genomes utilizing small, double-stranded RNAs to degrade target RNAs in a sequence-specific manner. Post-transcriptional gene silencing by these moieties can lead to degradation of both cellular and viral RNAs. It has recently been shown that double-stranded, small interfering RNAs (siRNAs) of 21-25 nucleotides can be transfected into relevant cells to target specific RNAs. This approach was utilized to inhibit human immunodeficiency virus type I (HIV-1) infection in human cells. siRNAs with homology to a motif in the mRNA that encodes for the HIV-1 chemokine coreceptor CXCR4 was utilized. Complementary studies via immunofluorescence microscopy and fluorescence-activated cell sorting demonstrated downregulation of CXCR4 from the surface of cells transfected with the specific siRNAs. As well, siRNAs without sequence homology to CXCR4 were used as controls and demonstrated no downregulation of CXCR4. siRNAs targeted to another chemokine coreceptor, APJ, showed specificity for downregulation of APJ but had no effects on CXCR4. Transfections with siRNAs targeting CXCR4 mRNA were shown to inhibit HIV-1 envelope fusion, which is relatively resistant to most viral inhibitors targeting chemokine coreceptors. The specificity of this effect was demonstrated by the inhibition of fusion by CXCR4-tropic and dual-tropic (CXCR4 and CCR5) envelope glycoproteins from HIV-1 on CXCR4+ indicator cells, but the lack of effects by siRNAs targeting CXCR4 mRNA on dual-tropic HIV-1 envelopes in CCR5+ indicator cells utilizing these fusion assays. Interestingly, siRNAs targeting CXCR4 selectively inhibited CXCR4-tropic cell-free virus infection of human cells but at only modest levels as compared to cell:cell fusion. siRNA may be a potential molecular therapeutic approach to alter a cellular cofactor critical for infection of human cells by relevant strains of HIV-1. The targeting of a cellular cofactor, rather than the HIV-1-specific mRNAs or genomic RNA, holds promise as the rapid mutational ability of the HIV-1 genome may obviate the potential clinical use of RNAi directly against this virus.
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Affiliation(s)
- N Zhou
- Division of Infectious Diseases and Environmental Medicine, Department of Medicine, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
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