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You searched for: Journal Nucleic acids research Remove constraint Journal: Nucleic acids research Publication Year 2011 Remove constraint Publication Year: 2011 Source 2011 v.39 no.14 Remove constraint Source: 2011 v.39 no.14
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1. Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors

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

2. Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme

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

3. A DNA minor groove electronegative potential genome map based on photo-chemical probing

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

4. A hyper-mutant of the unusual σ⁷⁰-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation

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

5. A novel DNA nuclease is stimulated by association with the GINS complex

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

6. A protein shuttle system to target RNA into mitochondria

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

7. A rapid, inexpensive yeast-based dual-fluorescence assay of programmed--1 ribosomal frameshifting for high-throughput screening

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

8. Biological insights from topology independent comparison of protein 3D structures

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

9. Cdt1 proteolysis is promoted by dual PIP degrons and is modulated by PCNA ubiquitylation

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

10. Cellular heat shock factor 1 positively regulates human immunodeficiency virus-1 gene expression and replication by two distinct pathways

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

11. Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

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

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

13. Crosstalk between c-Jun and TAp73α/β contributes to the apoptosis-survival balance

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

14. Cryptic splice sites and split genes

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

15. Differential usage of transcriptional start sites and polyadenylation sites in FMR1 premutation alleles

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

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

17. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

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

18. Efficient mutagenesis of the rhodopsin gene in rod photoreceptor neurons in mice

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

19. ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

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

20. Evidence for an evolutionary antagonism between Mrr and Type III modification systems

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