Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference.

abstract：:Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3'-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility using antisense oligonucl...

journal_title：Nucleic acids research

authors： Romero-López C,Barroso-Deljesus A,García-Sacristán A,Briones C,Berzal-Herranz A

更新日期：2012-12-01 00:00:00

abstract：:A repeated non-coding DNA sequence d(TTAGGG)n is present in the telomeric ends of all human chromosomes. These repeats can adopt multiple inter and intramolecular non-B-DNA conformations that may play an important role in biological processes. Two intramolecular structures of the telomeric oligonucleotide dAGGG(TTAGGG...

journal_title：Nucleic acids research

authors： He Y,Neumann RD,Panyutin IG

更新日期：2004-10-08 00:00:00

abstract：:We have investigated the response of the filamentous fungus Aspergillus nidulans to low, non-killing, doses of the alkylating agent MNNG (N-methyl-N'-nitro-N-nitrosoguanidine). Such treatment causes a substantial induction of DNA alkyltransferase activity, with the specific activity in treated cells increasing up to o...

journal_title：Nucleic acids research

authors： Baker SM,Margison GP,Strike P

更新日期：1992-02-25 00:00:00

abstract：:We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of th...

journal_title：Nucleic acids research

authors： Nielsen JT,Arar K,Petersen M

更新日期：2006-04-13 00:00:00

abstract：:The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls:...

journal_title：Nucleic acids research

authors： Jónsson SR,Haché G,Stenglein MD,Fahrenkrug SC,Andrésdóttir V,Harris RS

更新日期：2006-01-01 00:00:00

abstract：:Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...

journal_title：Nucleic acids research

authors： Wan C,Fu W,Jing H,Zhang N

更新日期：2019-02-20 00:00:00

abstract：:We have developed a new method for analysis of complex genetic systems by a combination of the Amplification Refractory Mutation System (ARMS) and Single-Strand Conformation Polymorphism (SSCP) analysis: ARMS-SSCP. Thus, a complex allelic series is subdivided into a number of groups by ARMS followed by the identificat...

journal_title：Nucleic acids research

authors： Lo YM,Patel P,Mehal WZ,Fleming KA,Bell JI,Wainscoat JS

更新日期：1992-03-11 00:00:00

abstract：:Eukaryotic elongation factor 1 A (eEF1A, formerly elongation factor-1 alpha) is an important component of the protein synthesis apparatus. Here we report the isolation and characterization of the cDNA sequence encoding rabbit eEF1A-2, an isoform of eEF1A, as well as a structural and functional comparison of the two ra...

journal_title：Nucleic acids research

authors： Kahns S,Lund A,Kristensen P,Knudsen CR,Clark BF,Cavallius J,Merrick WC

更新日期：1998-04-15 00:00:00

abstract：:A circular denaturation and restriction map of mitochondrial DNA from Neurospora crassa is presented. The map shows the position of all twelve fragments produced by restriction endonuclease Eco R I and the position of the largest Hin III fragment along the previously established map of AT-rich sequences. The two wild ...

journal_title：Nucleic acids research

authors： Bernard U,Goldthwaite C,Küntzel H

更新日期：1976-11-01 00:00:00

abstract：:Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computa...

journal_title：Nucleic acids research

authors： Zinoviev A,Kuroha K,Pestova TV,Hellen CUT

更新日期：2019-06-20 00:00:00

abstract：:To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predi...

journal_title：Nucleic acids research

authors： Schneider B,Cerný J,Svozil D,Cech P,Gelly JC,de Brevern AG

更新日期：2014-03-01 00:00:00

abstract：:Translesion synthesis (TLS) employs low fidelity polymerases to replicate past damaged DNA in a potentially error-prone process. Regulatory mechanisms that prevent TLS-associated mutagenesis are unknown; however, our recent studies suggest that the PCNA-binding protein Spartan plays a role in suppression of damage-ind...

journal_title：Nucleic acids research

authors： Kim MS,Machida Y,Vashisht AA,Wohlschlegel JA,Pang YP,Machida YJ

更新日期：2013-02-01 00:00:00

abstract：:Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity...

journal_title：Nucleic acids research

authors： O'Grady T,Wang X,Höner Zu Bentrup K,Baddoo M,Concha M,Flemington EK

更新日期：2016-10-14 00:00:00

abstract：:In this study, we show that silencing of CITED2 using small-hairpin RNA (shCITED2) induced DNA damage and reduction of ERCC1 gene expression in HEK293, HeLa and H1299 cells, even in the absence of cisplatin. In contrast, ectopic expression of ERCC1 significantly reduced intrinsic and induced DNA damage levels, and res...

journal_title：Nucleic acids research

authors： Liu YC,Chang PY,Chao CC

更新日期：2015-12-15 00:00:00

abstract：:RNA polymerase (RNAP) is a major target of gene regulation. Thermus thermophilus bacteriophage P23-45 encodes two RNAP binding proteins, gp39 and gp76, which shut off host gene transcription while allowing orderly transcription of phage genes. We previously reported the structure of the T. thermophilus RNAP•σA holoenz...

journal_title：Nucleic acids research

authors： Ooi WY,Murayama Y,Mekler V,Minakhin L,Severinov K,Yokoyama S,Sekine SI

更新日期：2018-01-09 00:00:00

abstract：:MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular ...

journal_title：Nucleic acids research

authors： Ali A,Veeranki SN,Tyagi S

更新日期：2014-07-01 00:00:00

abstract：:In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adap...

journal_title：Nucleic acids research

authors： Hardigan AA,Roberts BS,Moore DE,Ramaker RC,Jones AL,Myers RM

更新日期：2019-08-22 00:00:00

abstract：:BRCA1 expression is repressed by aberrant cytosine methylation in sporadic breast cancer. We hypothesized that aberrant cytosine methylation of the BRCA1 promoter was associated with the transcriptionally repressive effects of histone hypoacetylation and chromatin condensation. To address this question, we developed a...

journal_title：Nucleic acids research

authors： Rice JC,Futscher BW

更新日期：2000-09-01 00:00:00

abstract：:ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicy...

journal_title：Nucleic acids research

authors： Kumarevel T,Tanaka T,Umehara T,Yokoyama S

更新日期：2009-08-01 00:00:00

abstract：:PPARγ2 is a critical lineage-determining transcription factor that is essential for adipogenic differentiation. Here we report characterization of the three-dimensional structure of the PPARγ2 locus after the onset of adipogenic differentiation and the mechanisms by which it forms. We identified a differentiation-depe...

journal_title：Nucleic acids research

authors： LeBlanc SE,Wu Q,Lamba P,Sif S,Imbalzano AN

更新日期：2016-06-20 00:00:00

abstract：:Double-stranded oligonucleotides (ODNs) containing the consensus binding sequence of a transcription factor provide a rationally designed tool to manipulate gene expression at the transcriptional level by the decoy approach. However, modifications introduced into oligonucleotides to increase stability quite often do n...

journal_title：Nucleic acids research

authors： Crinelli R,Bianchi M,Gentilini L,Palma L,Sørensen MD,Bryld T,Babu RB,Arar K,Wengel J,Magnani M

更新日期：2004-03-29 00:00:00

abstract：:The transcription regulator, tvMyb1, is the first Myb family protein identified in Trichomonas vaginalis. Using an electrophoretic mobility shift assay, we defined the amino-acid sequence from Lys(35) to Ser(141) (tvMyb1(35-141)) as the minimal DNA-binding domain, encompassing two Myb-like DNA-binding motifs (designat...

journal_title：Nucleic acids research

authors： Lou YC,Wei SY,Rajasekaran M,Chou CC,Hsu HM,Tai JH,Chen C

更新日期：2009-04-01 00:00:00

abstract：:Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function....

journal_title：Nucleic acids research

authors： Richter F,Fonfara I,Bouazza B,Schumacher CH,Bratovič M,Charpentier E,Möglich A

更新日期：2016-11-16 00:00:00

abstract：:A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...

journal_title：Nucleic acids research

authors： Wang W,Shen P,Thiyagarajan S,Lin S,Palm C,Horvath R,Klopstock T,Cutler D,Pique L,Schrijver I,Davis RW,Mindrinos M,Speed TP,Scharfe C

更新日期：2011-01-01 00:00:00

abstract：:The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had ...

journal_title：Nucleic acids research

authors： Burland V,Plunkett G 3rd,Sofia HJ,Daniels DL,Blattner FR

更新日期：1995-06-25 00:00:00

abstract：:The Sleeping Beauty (SB) transposon is a promising gene transfer vector that integrates nonspecifically into host cell genomes. Herein, we attempt to direct transposon integration into predetermined DNA sites by coupling a site-specific DNA-binding domain (DBD) to the SB transposase. We engineered fusion proteins comp...

journal_title：Nucleic acids research

authors： Yant SR,Huang Y,Akache B,Kay MA

更新日期：2007-01-01 00:00:00

abstract：:Upon HIV-1 infection of a target cell, the viral reverse transcriptase (RT) copies the genomic RNA to synthesize the viral DNA. The genomic RNA is within the incoming HIV-1 core where it is coated by molecules of nucleocapsid (NC) protein that chaperones the reverse transcription process. Indeed, the RT chaperoning pr...

journal_title：Nucleic acids research

authors： Grigorov B,Bocquin A,Gabus C,Avilov S,Mély Y,Agopian A,Divita G,Gottikh M,Witvrouw M,Darlix JL

更新日期：2011-07-01 00:00:00

abstract：:The activity of MHC class II promoters depends upon conserved regulatory signals one of which, the extended X-box, contains in its X2 subregion a sequence related to the cAMP response element, CRE and to the TPA response element, TRE. Accordingly, X2 is recognized by the AP-1 factor and by other c-Jun or c-Fos contain...

journal_title：Nucleic acids research

authors： Neve Ombra M,Autiero M,DeLerma Barbaro A,Barretta R,Del Pozzo G,Guardiola J

更新日期：1993-04-25 00:00:00

abstract：:The promoter for the major coat protein gene of bacteriophage fd contains a unique sequence. TATAAT, in the non-transcribed region corresponding to the Pribnow box. A R-Hha I cleavage site which destroys functions is located five pairs upstream from the TATAAT sequence (fifteen base pairs upstream from the RNA initiat...

journal_title：Nucleic acids research

authors： Okamoto T,Sugimoto K,Sugisaki H,Takanami M

更新日期：1977-07-01 00:00:00

abstract：:A 2.1-kb cDNA clone representing a new member of the protease inhibitor family was isolated from a human liver cDNA library. The inhibitor, named human Leuserpin 2 (hLS2), comprises 480 amino acids and contains a leucine residue at its putative reactive center. HLS2 is about 25-28% homologous to three human members of...

journal_title：Nucleic acids research

authors： Ragg H

更新日期：1986-01-24 00:00:00