Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator.

abstract：:Many interacting proteins regulate and/or assist the activities of RAD51, a recombinase which plays a critical role in both DNA repair and meiotic recombination. Yeast two-hybrid screening of a human testis cDNA library revealed a new protein, RAD51AP2 (RAD51 Associated Protein 2), that interacts strongly with RAD51. ...

journal_title：Nucleic acids research

authors： Kovalenko OV,Wiese C,Schild D

更新日期：2006-01-01 00:00:00

abstract：:The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existin...

journal_title：Nucleic acids research

authors： Skrzypek MS,Nash RS,Wong ED,MacPherson KA,Hellerstedt ST,Engel SR,Karra K,Weng S,Sheppard TK,Binkley G,Simison M,Miyasato SR,Cherry JM

更新日期：2018-01-04 00:00:00

abstract：:The nucleotide sequence of a Pseudomonas trans-zeatin producing gene (ptz) from the pCK1 plasmid of Pseudomonas syringae pv. savastanoi strain 1006 has been determined. This gene confers upon E. coli the ability to synthesize and secrete several cytokinins including trans-zeatin, iso-pentenyladenine and their respecti...

journal_title：Nucleic acids research

authors： Powell GK,Morris RO

更新日期：1986-03-25 00:00:00

abstract：:Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translato...

journal_title：Nucleic acids research

authors： Liu W,Xiang L,Zheng T,Jin J,Zhang G

更新日期：2018-01-04 00:00:00

abstract：:The pac1+ gene of the fission yeast Schizosaccharomyces pombe is essential for viability and its overexpression induces sterility and suppresses mutations in the pat1+ and snm1+ genes. The pac1+ gene encodes a protein that is structurally similar to RNase III from Escherichia coli, but its normal function is unknown. ...

journal_title：Nucleic acids research

authors： Rotondo G,Frendewey D

更新日期：1996-06-15 00:00:00

abstract：:We have reported that an upstream stimulatory factor (USF) binding site is functional in transcription of the heme oxygenase-1 gene. In this study, we examined the role of USF in the induced state. By transient expression analyses with the chloramphenicol acetyl-transferase gene, we found that the USF binding site pla...

journal_title：Nucleic acids research

authors： Maeshima H,Sato M,Ishikawa K,Katagata Y,Yoshida T

更新日期：1996-08-01 00:00:00

abstract：:The abundance and complexity of total poly(A)+RNA of human normal unstimulated lymphocytes, PHA-stimulated and leukemic lymphocytes were examined using the cDNA-poly(A)+ RNA hybridization technique. It was found that in both PHA-stimulated and leukemic lymphocytes the complexity of total poly(A)+RNA is strongly reduce...

journal_title：Nucleic acids research

authors： Torelli G,Ferrari S,Donelli A,Cadossi R,Ferrari S,Bosi P,Torelli U

更新日期：1981-12-21 00:00:00

abstract：:Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein, which binds both single-stranded (ss) and double-stranded (ds) DNA and facilitates the formation of higher order protein-DNA complexes in vitro. LrpC binds at different sites within the same DNA molecule promoting intramolecular liga...

journal_title：Nucleic acids research

authors： López-Torrejón G,Martínez-Jiménez MI,Ayora S

更新日期：2006-01-10 00:00:00

abstract：:Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to dele...

journal_title：Nucleic acids research

authors： Kaboli S,Yamakawa T,Sunada K,Takagaki T,Sasano Y,Sugiyama M,Kaneko Y,Harashima S

更新日期：2014-09-01 00:00:00

abstract：:Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We f...

journal_title：Nucleic acids research

authors： Burch JB,Martinson HG

更新日期：1980-11-11 00:00:00

abstract：:Therapeutic oligonucleotides are often modified using the phosphorothioate (PS) backbone modification which enhances stability from nuclease mediated degradation. However, substituting oxygen in the phosphodiester backbone with sulfur introduce chirality into the backbone such that a full PS 16-mer oligonucleotide is ...

journal_title：Nucleic acids research

authors： Østergaard ME,De Hoyos CL,Wan WB,Shen W,Low A,Berdeja A,Vasquez G,Murray S,Migawa MT,Liang XH,Swayze EE,Crooke ST,Seth PP

更新日期：2020-02-28 00:00:00

abstract：:A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...

journal_title：Nucleic acids research

authors： Reimann V,Alkhnbashi OS,Saunders SJ,Scholz I,Hein S,Backofen R,Hess WR

更新日期：2017-01-25 00:00:00

abstract：:Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we discover an HRP2-DPF3a-BAF epigenetic pathway that coordinates methylated histone H3 ly...

journal_title：Nucleic acids research

authors： Zhu X,Lan B,Yi X,He C,Dang L,Zhou X,Lu Y,Sun Y,Liu Z,Bai X,Zhang K,Li B,Li MJ,Chen Y,Zhang L

更新日期：2020-07-09 00:00:00

abstract：:Nonsense-mediated mRNA decay (NMD) is a molecular pathway of mRNA surveillance that ensures rapid degradation of mRNAs containing premature translation termination codons (PTCs) in eukaryotes. NMD has been shown to also regulate normal gene expression and thus emerged as one of the key post-transcriptional mechanisms ...

journal_title：Nucleic acids research

authors： Viegas MH,Gehring NH,Breit S,Hentze MW,Kulozik AE

更新日期：2007-01-01 00:00:00

abstract：:SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human s...

journal_title：Nucleic acids research

authors： Dogan RI,Getoor L,Wilbur WJ,Mount SM

更新日期：2007-07-01 00:00:00

abstract：:Detailed models are presented for the triple-stranded polynucleotide helices of poly (U)-poly (A)-poly (U) (two forms), poly (U)-poly d (A) -poly (U), poly d(C)-poly d(I)-poly d(C), poly d(T)-polyd(A)-poly d(T) and poly (I)-poly (A)-poly (I). The models were genrated using a computerized, linked-atom procedure which p...

journal_title：Nucleic acids research

authors： Arnott S,Bond PJ,Selsing E,Smith PJ

更新日期：1976-10-01 00:00:00

abstract：:A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three c...

journal_title：Nucleic acids research

authors： Guo FB,Ou HY,Zhang CT

更新日期：2003-03-15 00:00:00

abstract：:Plant mitochondrial genomes show much more evolutionary plasticity than those of animals. We analysed the first mitochondrial DNA (mtDNA) of a lycophyte, the quillwort Isoetes engelmannii, which is separated from seed plants by more than 350 million years of evolution. The Isoetes mtDNA is particularly rich in recombi...

journal_title：Nucleic acids research

authors： Grewe F,Viehoever P,Weisshaar B,Knoop V

更新日期：2009-08-01 00:00:00

abstract：:Initial steps in the synthesis of functional tRNAs require 5'- and 3'-processing of precursor tRNAs (pre-tRNAs), which in yeast mitochondria are achieved by two endonucleases, RNase P and RNase Z. In this study, using a combination of detergent-free Blue Native Gel Electrophoresis, proteomics and in vitro testing of p...

journal_title：Nucleic acids research

authors： Daoud R,Forget L,Lang BF

更新日期：2012-02-01 00:00:00

abstract：:By subtractive screening of a library made from mRNA of lipopolysaccharide (LPS)-stimulated mouse B lymphocytes we isolated cDNA-clones encoding the ribosomal protein L7. Human L7 mRNA was cloned from activated T-lymphocytes. Although no specific function of L7 in the translation apparatus is known as yet, it should b...

journal_title：Nucleic acids research

authors： Hemmerich P,von Mikecz A,Neumann F,Sözeri O,Wolff-Vorbeck G,Zoebelein R,Krawinkel U

更新日期：1993-01-25 00:00:00

abstract：:The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...

journal_title：Nucleic acids research

authors： Faber SW,Wilcox KW

更新日期：1988-01-25 00:00:00

abstract：:We have determined the three-dimensional structure of a non-selfcomplementary nonanucleotide duplex which contains an abasic (apyrimidinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assigned by NOESY, COSY and 2DQF spectra in D2O and...

journal_title：Nucleic acids research

authors： Cuniasse P,Sowers LC,Eritja R,Kaplan B,Goodman MF,Cognet JA,LeBret M,Guschlbauer W,Fazakerley GV

更新日期：1987-10-12 00:00:00

abstract：:Type II CRISPR-Cas9 RNA-guided nucleases are widely used for genome engineering. Type II-A SpCas9 protein from Streptococcus pyogenes is the most investigated and highly used enzyme of its class. Nevertheless, it has some drawbacks, including a relatively big size, imperfect specificity and restriction to DNA targets ...

journal_title：Nucleic acids research

authors： Fedorova I,Arseniev A,Selkova P,Pobegalov G,Goryanin I,Vasileva A,Musharova O,Abramova M,Kazalov M,Zyubko T,Artamonova T,Artamonova D,Shmakov S,Khodorkovskii M,Severinov K

更新日期：2020-02-28 00:00:00

abstract：:Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...

journal_title：Nucleic acids research

authors： Ibba M,Sever S,Praetorius-Ibba M,Söll D

更新日期：1999-09-15 00:00:00

abstract：:An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migra...

journal_title：Nucleic acids research

authors： Shen W,Sun H,De Hoyos CL,Bailey JK,Liang XH,Crooke ST

更新日期：2017-10-13 00:00:00

abstract：:The goal of this study was to address antiparallel triplex formation at duplex targets that do not conform to a strict oligopurine.oligopyrimidine motif. We focused on the ability of natural bases and base analogs incorporated into oligonucleotide third strands to bind to so-called CG inversions. These are sites where...

journal_title：Nucleic acids research

authors： Durland RH,Rao TS,Revankar GR,Tinsley JH,Myrick MA,Seth DM,Rayford J,Singh P,Jayaraman K

更新日期：1994-08-11 00:00:00

abstract：:A synthetic gene encoding the Schizophyllum commune xylanase XynA was constructed by a novel PCR-based procedure. Three long oligonucleotides were synthesized and used in combination with flanking PCR primers to generate a 607 base pair gene which contained 31 unique locations for restriction enzyme cleavage. The amin...

journal_title：Nucleic acids research

authors： Graham RW,Atkinson T,Kilburn DG,Miller RC Jr,Warren RA

更新日期：1993-10-25 00:00:00

abstract：:Histone H3K4 methylation is an epigenetic mark associated with actively transcribed genes. This modification is catalyzed by the mixed lineage leukaemia (MLL) family of histone methyltransferases including MLL1, MLL2, MLL3, MLL4, SET1A and SET1B. The catalytic activity of this family is dependent on interactions with ...

journal_title：Nucleic acids research

authors： Kaustov L,Lemak A,Wu H,Faini M,Fan L,Fang X,Zeng H,Duan S,Allali-Hassani A,Li F,Wei Y,Vedadi M,Aebersold R,Wang Y,Houliston S,Arrowsmith CH

更新日期：2019-09-26 00:00:00

abstract：:Sequence heterogeneity is a common characteristic of RNA viruses that is often referred to as sub-populations or quasispecies. Traditional techniques used for assembly of short sequence reads produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity. Here, we introduce a novel algorithm ...

journal_title：Nucleic acids research

authors： Karagiannis K,Simonyan V,Chumakov K,Mazumder R

更新日期：2017-11-02 00:00:00

abstract：:The multifunctional RNA-dependent RNA polymerase L protein of vesicular stomatitis virus catalyzes unconventional pre-mRNA capping via the covalent enzyme-pRNA intermediate formation, which requires the histidine-arginine (HR) motif in the polyribonucleotidyltransferase domain. Here, the effects of cap-defective mutat...

journal_title：Nucleic acids research

authors： Ogino T

更新日期：2014-10-29 00:00:00