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Nucleic acids research
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2011 v.39 no.14
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- Author:
- Vallejos, Maricarmen; Deforges, Jules; Plank, Terra-Dawn M.; Letelier, Alejandro; Ramdohr, Pablo; Abraham, Christopher G.; Valiente-Echeverría, Fernando; Kieft, Jeffrey S.; Sargueil, Bruno; López-Lastra, Marcelo
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6186-6200
- ISSN:
- 0305-1048
- Subject:
- Human immunodeficiency virus 1; RNA; cell cycle; models; mutation; ribosomes; transactivators; translation (genetics)
- Abstract:
- ... The 5' leader of the human immunodeficiency virus type 1 (HIV-1) genomic RNA harbors an internal ribosome entry site (IRES) that is functional during the G2/M phase of the cell cycle. Here we show that translation initiation mediated by the HIV-1 IRES requires the participation of trans-acting cellular factors other than the canonical translational machinery. We used 'standard' chemical and enzyma ...
- DOI:
- 10.1093/nar/gkr189
- PubMed:
- 21482538
- PubMed Central:
- PMC3152342
- http://dx.doi.org/10.1093/nar/gkr189
- Author:
- DeAbreu, Diane M.; Olive, Joan E.; Collins, Richard A.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6223-6228
- ISSN:
- 0305-1048
- Subject:
- Neurospora; magnesium; mutants; mutation; nucleotides; ribozymes
- Abstract:
- ... Many RNAs contain tertiary interactions that contribute to folding the RNA into its functional 3D structure. In the VS ribozyme, a tertiary loop-loop kissing interaction involving stem-loops I and V is also required to rearrange the secondary structure of stem-loop I such that nucleotides at the base of stem I, which contains the cleavage-ligation site, can adopt the conformation required for acti ...
- DOI:
- 10.1093/nar/gkr250
- PubMed:
- 21507887
- PubMed Central:
- PMC3152364
- http://dx.doi.org/10.1093/nar/gkr250
- Author:
- Lindemose, Søren; Nielsen, Peter Eigil; Hansen, Morten; Møllegaard, Niels Erik
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6269-6276
- ISSN:
- 0305-1048
- Subject:
- DNA; RNA; algorithms; binding sites; gene expression; genome; models; nucleosomes
- Abstract:
- ... The double-stranded DNA of the genome contains both sequence information directly relating to the protein and RNA coding as well as functional and structural information relating to protein recognition. Only recently is the importance of DNA shape in this recognition process being fully appreciated, and it also appears that minor groove electronegative potential may contribute significantly in gui ...
- DOI:
- 10.1093/nar/gkr204
- PubMed:
- 21478164
- PubMed Central:
- PMC3152351
- http://dx.doi.org/10.1093/nar/gkr204
- Author:
- del Peso-Santos, Teresa; Bernardo, Lisandro M.D.; Skärfstad, Eleonore; Holmfeldt, Linda; Togneri, Peter; Shingler, Victoria
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 5853-5865
- ISSN:
- 0305-1048
- Subject:
- DNA-directed RNA polymerase; energy; metabolism; mutagenesis; nucleic acids; phenolic compounds
- Abstract:
- ... The activities of promoters can be temporally and conditionally regulated by mechanisms other than classical DNA-binding repressors and activators. One example is the inherently weak σ⁷⁰-dependent Pr promoter that ultimately controls catabolism of phenolic compounds. The activity of Pr is up-regulated through the joint action of ppGpp and DksA that enhance the performance of RNA polymerase at this ...
- DOI:
- 10.1093/nar/gkr167
- PubMed:
- 21447563
- PubMed Central:
- PMC3152329
- http://dx.doi.org/10.1093/nar/gkr167
- Author:
- Li, Zhuo; Pan, Miao; Santangelo, Thomas J.; Chemnitz, Wiebke; Yuan, Wei; Edwards, James L.; Hurwitz, Jerard; Reeve, John N.; Kelman, Zvi
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6114-6123
- ISSN:
- 0305-1048
- Subject:
- DNA; DNA replication; DNA-directed DNA polymerase; Thermococcus kodakarensis
- Abstract:
- ... Chromosomal DNA replication requires the spatial and temporal coordination of the activities of several complexes that constitute the replisome. A previously uncharacterized protein, encoded by TK1252 in the archaeon Thermococcus kodakaraensis, was shown to stably interact with the archaeal GINS complex in vivo, a central component of the archaeal replisome. Here, we document that this protein (TK ...
- DOI:
- 10.1093/nar/gkr181
- PubMed:
- 21459845
- PubMed Central:
- PMC3152336
- http://dx.doi.org/10.1093/nar/gkr181
- Author:
- Sieber, François; Placido, Antonio; El Farouk-Ameqrane, Samira; Duchêne, Anne-Marie; Maréchal-Drouard, Laurence
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. e96
- ISSN:
- 0305-1048
- Subject:
- RNA transport; mammals; messenger RNA; mitochondria; transfer RNA
- Abstract:
- ... Mitochondria play a key role in essential cellular functions. A deeper understanding of mitochondrial molecular processes is hampered by the difficulty of incorporating foreign nucleic acids into organelles. Mitochondria of most eukaryotic species import cytosolic tRNAs. Based on this natural process, we describe here a powerful shuttle system to internalize several types of RNAs into isolated mit ...
- DOI:
- 10.1093/nar/gkr380
- PubMed:
- 21596779
- PubMed Central:
- PMC3152368
- http://dx.doi.org/10.1093/nar/gkr380
- Author:
- Rakauskaitė, Rasa; Liao, Pei-Yu; Rhodin, Michael H.J.; Lee, Kelvin; Dinman, Jonathan D.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. e97
- ISSN:
- 0305-1048
- Subject:
- RNA viruses; Retroviridae; Saccharomyces cerevisiae; drugs; fluorescence; mammals; messenger RNA; protein synthesis; ribosomes; screening; therapeutics; viral proteins; viruses; yeasts
- Abstract:
- ... Programmed -1 ribosomal frameshifting (-1 PRF) is a mechanism that directs elongating ribosomes to shift-reading frame by 1 base in the 5' direction that is utilized by many RNA viruses. Importantly, rates of -1 PRF are fine-tuned by viruses, including Retroviruses, Coronaviruses, Flavivriuses and in two endogenous viruses of the yeast Saccharomyces cerevisiae, to deliver the correct ratios of dif ...
- DOI:
- 10.1093/nar/gkr382
- PubMed:
- 21602263
- PubMed Central:
- PMC3152369
- http://dx.doi.org/10.1093/nar/gkr382
- Author:
- Nguyen, Minh N.; Madhusudhan, M.S.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. e94
- ISSN:
- 0305-1048
- Subject:
- RNA; algorithms; amino acids; binding sites; chemical elements; geometry; molecular biology; proteins; solvents; topology
- Abstract:
- ... Comparing and classifying the three-dimensional (3D) structures of proteins is of crucial importance to molecular biology, from helping to determine the function of a protein to determining its evolutionary relationships. Traditionally, 3D structures are classified into groups of families that closely resemble the grouping according to their primary sequence. However, significant structural simila ...
- DOI:
- 10.1093/nar/gkr348
- PubMed:
- 21596786
- PubMed Central:
- PMC3152366
- http://dx.doi.org/10.1093/nar/gkr348
- Author:
- Guarino, Estrella; Shepherd, Marianne E.A.; Salguero, Israel; Hua, Hui; Deegan, Rachel S.; Kearsey, Stephen E.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 5978-5990
- ISSN:
- 0305-1048
- Subject:
- Animalia; DNA; DNA damage; DNA repair; DNA replication; Schizosaccharomyces pombe; enzymes; interphase; proliferating cell nuclear antigen; proteolysis
- Abstract:
- ... Cdt1 plays a critical role in DNA replication regulation by controlling licensing. In Metazoa, Cdt1 is regulated by CRL4Cdt²-mediated ubiquitylation, which is triggered by DNA binding of proliferating cell nuclear antigen (PCNA). We show here that fission yeast Cdt1 interacts with PCNA in vivo and that DNA loading of PCNA is needed for Cdt1 proteolysis after DNA damage and in S phase. Activation o ...
- DOI:
- 10.1093/nar/gkr222
- PubMed:
- 21493688
- PubMed Central:
- PMC3152358
- http://dx.doi.org/10.1093/nar/gkr222
- Author:
- Rawat, Pratima; Mitra, Debashis
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 5879-5892
- ISSN:
- 0305-1048
- Subject:
- HIV infections; Human immunodeficiency virus 1; gene expression; heat shock proteins; heat stress; nucleic acids; ultraviolet radiation; virus replication
- Abstract:
- ... Human immunodeficiency virus-1 (HIV-1) infection leads to changes in cellular gene expression, which in turn tend to modulate viral gene expression and replication. Cellular heat shock proteins (HSPs) are induced upon heat shock, UV irradiation and microbial or viral infections. We have reported earlier Nef-dependent induction of HSP40 leading to increased HIV-1 gene expression; however, the mecha ...
- DOI:
- 10.1093/nar/gkr198
- PubMed:
- 21459854
- PubMed Central:
- PMC3152347
- http://dx.doi.org/10.1093/nar/gkr198
- Author:
- Bundschuh, R.; Altmüller, J.; Becker, C.; Nürnberg, P.; Gott, J.M.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6044-6055
- ISSN:
- 0305-1048
- Subject:
- Physarum polycephalum; complementary DNA; databases; genes; high-throughput nucleotide sequencing; messenger RNA; mitochondria; mitochondrial RNA; mitochondrial genome; proteins; transcription (genetics); transcriptome
- Abstract:
- ... RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides also added at specific sites. The existence of insertional editing makes gene identification difficult and localization of editing sites has relied upon characterization of individual cDNAs. We have now determined the ...
- DOI:
- 10.1093/nar/gkr180
- PubMed:
- 21478163
- PubMed Central:
- PMC3152335
- http://dx.doi.org/10.1093/nar/gkr180
12. Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease
- Author:
- Grizot, Sylvestre; Duclert, Aymeric; Thomas, Séverine; Duchateau, Philippe; Pâques, Frédéric
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6124-6136
- ISSN:
- 0305-1048
- Subject:
- DNA; amino acids; engineering; gene targeting; genes; loci; mutation; scaffolding proteins
- Abstract:
- ... Homing endonucleases (HE) have emerged as precise tools for achieving gene targeting events. Redesigned HEs with tailored specificities can be used to cleave new sequences, thereby considerably expanding the number of targetable genes and loci. With HEs, as well as with other protein scaffolds, context dependence of DNA/protein interaction patterns remains one of the major limitations for rational ...
- DOI:
- 10.1093/nar/gkr186
- PubMed:
- 21482539
- PubMed Central:
- PMC3152339
- http://dx.doi.org/10.1093/nar/gkr186
- Author:
- Koeppel, Max; van Heeringen, Simon J.; Kramer, Daniela; Smeenk, Leonie; Janssen-Megens, Eva; Hartmann, Marianne; Stunnenberg, Hendrik G.; Lohrum, Marion
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6069-6085
- ISSN:
- 0305-1048
- Subject:
- apoptosis; binding sites; chromatin; gene expression; gene expression regulation; genes; messenger RNA; precipitin tests; signal transduction; transcription (genetics)
- Abstract:
- ... The p53-family member p73 plays a role in various cellular signaling pathways during development and growth control and it can have tumor suppressor properties. Several isoforms of p73 exist with considerable differences in their function. Whereas the functions of the N-terminal isoforms (TA and ΔNp73) and their opposing pro- and antiapoptotic roles have become evident, the functional differences ...
- DOI:
- 10.1093/nar/gkr028
- PubMed:
- 21459846
- PubMed Central:
- PMC3152320
- http://dx.doi.org/10.1093/nar/gkr028
- Author:
- Kapustin, Yuri; Chan, Elcie; Sarkar, Rupa; Wong, Frederick; Vorechovsky, Igor; Winston, Robert M.; Tatusova, Tatiana; Dibb, Nick J.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 5837-5844
- ISSN:
- 0305-1048
- Subject:
- evolution; eukaryotic cells; mutation; genetic disorders; nucleic acids; exons; introns
- Abstract:
- ... We describe a new program called cryptic splice finder (CSF) that can reliably identify cryptic splice sites (css), so providing a useful tool to help investigate splicing mutations in genetic disease. We report that many css are not entirely dormant and are often already active at low levels in normal genes prior to their enhancement in genetic disease. We also report a fascinating correlation be ...
- DOI:
- 10.1093/nar/gkr203
- PubMed:
- 21470962
- PubMed Central:
- PMC3152350
- http://dx.doi.org/10.1093/nar/gkr203
- Author:
- Tassone, Flora; De Rubeis, Silvia; Carosi, Chiara; La Fata, Giorgio; Serpa, Gisele; Raske, Christopher; Willemsen, Rob; Hagerman, Paul J.; Bagni, Claudia
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6172-6185
- ISSN:
- 0305-1048
- Subject:
- 3' untranslated regions; alleles; ataxia (disorder); autism; brain; disease course; females; humans; mice; mutation; neurodegenerative diseases; phenotype; transcription (genetics)
- Abstract:
- ... 5'- and 3'-untranslated regions (UTRs) are important regulators of gene expression and play key roles in disease progression and susceptibility. The 5'-UTR of the fragile X mental retardation 1 (FMR1) gene contains a CGG repeat element that is expanded (>200 CGG repeats; full mutation) and methylated in fragile X syndrome (FXS), the most common form of inherited intellectual disability (ID) and kn ...
- DOI:
- 10.1093/nar/gkr100
- PubMed:
- 21478165
- PubMed Central:
- PMC3152321
- http://dx.doi.org/10.1093/nar/gkr100
16. Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant
- Author:
- Tsao, Douglas; Shabalina, Svetlana A.; Gauthier, Josée; Dokholyan, Nikolay V.; Diatchenko, Luda
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6201-6212
- ISSN:
- 0305-1048
- Subject:
- alleles; catechol O-methyltransferase; cognition; emotions; genetic variation; haplotypes; human population; messenger RNA; pain; prediction; probability; protein synthesis; start codon; translation (genetics)
- Abstract:
- ... Catechol-O-methyltransferase (COMT) is a major enzyme controlling catecholamine levels that plays a central role in cognition, affective mood and pain perception. There are three common COMT haplotypes in the human population reported to have functional effects, divergent in two synonymous and one nonsynonymous position. We demonstrate that one of the haplotypes, carrying the non-synonymous variat ...
- DOI:
- 10.1093/nar/gkr165
- PubMed:
- 21486747
- PubMed Central:
- PMC3152328
- http://dx.doi.org/10.1093/nar/gkr165
- Author:
- Galante, Pedro A.F.; Parmigiani, Raphael B.; Zhao, Qi; Caballero, Otávia L.; de Souza, Jorge E.; Navarro, Fábio C.P.; Gerber, Alexandra L.; Nicolás, Marisa F.; Salim, Anna Christina M.; Silva, Ana Paula M.; Edsall, Lee; Devalle, Sylvie; Almeida, Luiz G.; Ye, Zhen; Kuan, Samantha; Pinheiro, Daniel G.; Tojal, Israel; Pedigoni, Renato G.; de Sousa, Rodrigo G.M.A.; Oliveira, Thiago Y.K.; de Paula, Marcelo G.; Ohno-Machado, Lucila; Kirkness, Ewen F.; Levy, Samuel; da Silva, Wilson A. Jr.; Vasconcelos, Ana Tereza R.; Ren, Bing; Zago, Marco Antonio; Strausberg, Robert L.; Simpson, Andrew J.G.; de Souza, Sandro J.; Camargo, Anamaria A.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 6056-6068
- ISSN:
- 0305-1048
- Subject:
- breast neoplasms; genes; mutagens; mutation; neoplastic cell transformation; nucleic acids; patients; protein-protein interactions; signal transduction
- Abstract:
- ... Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient a ...
- DOI:
- 10.1093/nar/gkr221
- PubMed:
- 21493686
- PubMed Central:
- PMC3152357
- http://dx.doi.org/10.1093/nar/gkr221
- Author:
- Chan, Fung; Hauswirth, William W.; Wensel, Theodore G.; Wilson, John H.
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 5955-5966
- ISSN:
- 0305-1048
- Subject:
- Dependoparvovirus; annealing; loci; humans; neurons; rhodopsin; mutagenesis; homologous recombination; mice; DNA repair; nucleic acids; exons
- Abstract:
- ... Dominant mutations in the rhodopsin gene, which is expressed in rod photoreceptor cells, are a major cause of the hereditary-blinding disease, autosomal dominant retinitis pigmentosa. Therapeutic strategies designed to edit such mutations will likely depend on the introduction of double-strand breaks and their subsequent repair by homologous recombination or non-homologous end joining. At present, ...
- DOI:
- 10.1093/nar/gkr196
- PubMed:
- 21478169
- PubMed Central:
- PMC3152346
- http://dx.doi.org/10.1093/nar/gkr196
- Author:
- Cai, Yunpeng; Sun, Yijun
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. e95
- ISSN:
- 0305-1048
- Subject:
- algorithms; cluster analysis; data collection; genetic distance; humans; intestinal microorganisms; microbial communities; nucleotide sequences; ribosomal RNA
- Abstract:
- ... Taxonomy-independent analysis plays an essential role in microbial community analysis. Hierarchical clustering is one of the most widely employed approaches to finding operational taxonomic units, the basis for many downstream analyses. Most existing algorithms have quadratic space and computational complexities, and thus can be used only for small or medium-scale problems. We propose a new online ...
- DOI:
- 10.1093/nar/gkr349
- PubMed:
- 21596775
- PubMed Central:
- PMC3152367
- http://dx.doi.org/10.1093/nar/gkr349
- Author:
- Tesfazgi Mebrhatu, Mehari; Wywial, Ewa; Ghosh, Anirban; Michiels, Chris W.; Lindner, Ariel B.; Taddei, François; Bujnicki, Janusz M.; Van Melderen, Laurence; Aertsen, Abram
- Source:
- Nucleic acids research 2011 v.39 no.14 pp. 5991-6001
- ISSN:
- 0305-1048
- Subject:
- DNA; Escherichia coli; Salmonella Typhimurium; antagonism; databases; epigenetics; genes; genotoxicity; loci; methyltransferases; restriction endonucleases; screening
- Abstract:
- ... The Mrr protein of Escherichia coli is a laterally acquired Type IV restriction endonuclease with specificity for methylated DNA. While Mrr nuclease activity can be elicited by high-pressure stress in E. coli MG1655, its (over)expression per se does not confer any obvious toxicity. In this study, however, we discovered that Mrr of E. coli MG1655 causes distinct genotoxicity when expressed in Salmo ...
- DOI:
- 10.1093/nar/gkr219
- PubMed:
- 21504983
- PubMed Central:
- PMC3152355
- http://dx.doi.org/10.1093/nar/gkr219
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