NF-kappaB controls the global pro-inflammatory response in endothelial cells: evidence for the regulation of a pro-atherogenic program.

abstract：:Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 ca...

journal_title：Nucleic acids research

authors： Das D,Clark TA,Schweitzer A,Yamamoto M,Marr H,Arribere J,Minovitsky S,Poliakov A,Dubchak I,Blume JE,Conboy JG

更新日期：2007-01-01 00:00:00

abstract：:This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...

journal_title：Nucleic acids research

authors： Benham CJ

更新日期：1987-12-10 00:00:00

abstract：:Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytopl...

journal_title：Nucleic acids research

authors： Dalia TN,Yoon SH,Galli E,Barre FX,Waters CM,Dalia AB

更新日期：2017-07-07 00:00:00

abstract：:We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify th...

journal_title：Nucleic acids research

authors： Moretti S,Reinier F,Poirot O,Armougom F,Audic S,Keduas V,Notredame C

更新日期：2006-07-01 00:00:00

abstract：:Defining syntenic relationships among orthologous gene clusters is a frequent undertaking of biologists studying organismal evolution through comparative genomic approaches. With the increasing availability of genome data made possible through next-generation sequencing technology, there is a growing need for user-fri...

journal_title：Nucleic acids research

authors： Veltri D,Wight MM,Crouch JA

更新日期：2016-07-08 00:00:00

abstract：:We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', su...

journal_title：Nucleic acids research

authors： Todd AK,Neidle S

更新日期：2008-05-01 00:00:00

abstract：:The 'sandwich' binding format, which uses two reagents that can bind simultaneously to a given analyte, is the gold standard in diagnostics and many biochemical techniques. One of the bottlenecks in creating a sandwich assay is identifying pairs of reagents that bind non-competitively to the target. To bridge this gap...

journal_title：Nucleic acids research

authors： Gorman KT,Roby LC,Giuffre A,Huang R,Kay BK

更新日期：2017-10-13 00:00:00

abstract：:The pattern of sites for cleavage mediated by topoisomerase II was determined in 830 kb of cloned DNA from the Drosophila X chromosome, with the objectives of comparing it with mapped structural and functional landmarks and examining if the correlations with such landmarks reported in individual loci can be generalize...

journal_title：Nucleic acids research

authors： Miassod R,Razin SV,Hancock R

更新日期：1997-06-01 00:00:00

abstract：:Restriction fragments of T7 DNA which selectively bind E. coli RNA polymerase have been identified. These include fragments located close to the beginning of gene 1 where according to Minkley and Pribnow (1973) there is a promoter called C. The smallest fragment from this region which binds RNA polymerase has been seq...

journal_title：Nucleic acids research

authors： McConnell DJ

更新日期：1979-02-01 00:00:00

abstract：:Double-stranded (ds) oligodeoxynucleotides (29mers) containing an O6-ethylguanine (O6-EtGua) flanked 5' and 3' by different bases (5'..TGT..3'; 5'..CGG..3', 5'..GGT..3'; 5'..GGG..3'; 5'..GGA..3') were synthesized to investigate the binding and repair characteristics of recombinant human O6-alkylguanine-DNA alkyltransf...

journal_title：Nucleic acids research

authors： Bender K,Federwisch M,Loggen U,Nehls P,Rajewsky MF

更新日期：1996-06-01 00:00:00

abstract：:eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes. However the extent to which specific mRNA targets are regulated by 4E-BPs remains unknown. We performed translational profiling by microarray analysis of polysome and monosome associated mRNAs in wild-type and mutant cells to identify mRNAs i...

journal_title：Nucleic acids research

authors： Cridge AG,Castelli LM,Smirnova JB,Selley JN,Rowe W,Hubbard SJ,McCarthy JE,Ashe MP,Grant CM,Pavitt GD

更新日期：2010-12-01 00:00:00

abstract：:Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified...

journal_title：Nucleic acids research

authors： Das T,Park JK,Park J,Kim E,Rape M,Kim EE,Song EJ

更新日期：2017-05-05 00:00:00

abstract：:A DNA methylase has been purified 270-fold from HeLa cell nuclei by chromatography on DEAE-cellulose, phosphocellulose, and hydroxyapatite. The enzyme transfers methyl groups from S-adenosyl-L-methionine to cytosine residues in DNA. The sole product of the reaction has been identified as 5-methylcytosine. The enzyme i...

journal_title：Nucleic acids research

authors： Roy PH,Weissbach A

更新日期：1975-10-01 00:00:00

abstract：:To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, c...

journal_title：Nucleic acids research

authors： Chen YB,Chattopadhyay A,Bergen P,Gadd C,Tannery N

更新日期：2007-01-01 00:00:00

abstract：:Isolated yeast mitochondria incorporate added UTP into RNA. Amongst the products formed are the two rRNAs, 4S RNA and several components presumed to be mRNAs. In omega+ strains (containing an intervening sequence in the 21S rRNA gene) besides mature 21S rRNA a transcript could be detected still containing nucleotide s...

journal_title：Nucleic acids research

authors： Groot GS,van Harten-Loosbroek N,van Ommen GJ,Pijst HL

更新日期：1981-12-11 00:00:00

abstract：:While most of the recent improvements in multiple sequence alignment accuracy are due to better use of vertical information, which include the incorporation of consistency-based pairwise alignments and the use of profile alignments, we observe that it is possible to further improve accuracy by taking into account alig...

journal_title：Nucleic acids research

authors： Lu Y,Sze SH

更新日期：2009-02-01 00:00:00

abstract：:Homologous recombination (HR) is important in repairing errors of replication and other forms of DNA damage. In mammalian cells, potential templates include the homologous chromosome, and after DNA replication, the sister chromatid. Previous work has shown that the mammalian recombination machinery is organized to sup...

journal_title：Nucleic acids research

authors： Read LR,Raynard SJ,Rukść A,Baker MD

更新日期：2004-02-20 00:00:00

abstract：:Laser-Raman spectra of poly(rI) show the formation of an ordered complex in aqueous solutions of high ionic strength. This structure exhibits the A-helix geometry, contains stacked bases and is apparently stabilized by specific hydrogen bonding involving hypoxanthine C6=0 groups. Thermal dissociation of the poly(rI) c...

journal_title：Nucleic acids research

authors： Chou CH,Thomas GJ Jr,Arnott S,Smith PJ

更新日期：1977-07-01 00:00:00

abstract：:The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...

journal_title：Nucleic acids research

authors： Hain J,Reiter WD,Hüdepohl U,Zillig W

更新日期：1992-10-25 00:00:00

abstract：:No analogous nucleoside triphosphate was found which acts as well as ATP in binding to and supporting catalysis of leucyl-tRNA synthetase from Escherichia coli MRE 600. However, there are numerous nucleotides which are able to replace ATP, but with lower efficiency. The 6-amino group of the adenine ring and the 2'-hyd...

journal_title：Nucleic acids research

authors： Marutzky R,Flossdorf J,Kula MR

更新日期：1976-08-01 00:00:00

abstract：:Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...

journal_title：Nucleic acids research

authors： Iwamura Y,Sakai M,Muramatsu M

更新日期：1982-07-24 00:00:00

abstract：:An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...

journal_title：Nucleic acids research

authors： Paccanaro A,Casbon JA,Saqi MA

更新日期：2006-03-17 00:00:00

abstract：:The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...

journal_title：Nucleic acids research

authors： Mukherjee S,Stamatis D,Bertsch J,Ovchinnikova G,Katta HY,Mojica A,Chen IA,Kyrpides NC,Reddy T

更新日期：2019-01-08 00:00:00

abstract：:cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequen...

journal_title：Nucleic acids research

authors： Hoskins RA,Stapleton M,George RA,Yu C,Wan KH,Carlson JW,Celniker SE

更新日期：2005-12-02 00:00:00

abstract：:Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available s...

journal_title：Nucleic acids research

authors： Parameswaran P,Jalili R,Tao L,Shokralla S,Gharizadeh B,Ronaghi M,Fire AZ

更新日期：2007-01-01 00:00:00

abstract：:Exonic splicing enhancer (ESE) sequences are bound by serine & arginine-rich (SR) proteins, which in turn enhance the recruitment of splicing factors. It was inferred from measurements of splicing around twenty years ago that Drosophila doublesex ESEs are bound stably by SR proteins, and that the bound proteins intera...

journal_title：Nucleic acids research

authors： Jobbins AM,Reichenbach LF,Lucas CM,Hudson AJ,Burley GA,Eperon IC

更新日期：2018-03-16 00:00:00

abstract：:We previously reported that O4-alkyl dTTPs could replace, for short times, dTTP in polymer synthesis [Singer et al., PNAS 83, 26-32, 1986]. The reasons for such early termination of synthesis could be either proofreading or the eventual formation of weakly paired primer termini. Utilizing the known 3'----5' exonucleol...

journal_title：Nucleic acids research

authors： Singer B

更新日期：1986-08-26 00:00:00

abstract：:This work describes the organization, at the nucleotide sequence level, of genes flanking the junctions of the large single copy regions and the inverted repeats of Spinacia oleracea (spinach) and Nicotiana debneyi chloroplast DNAs. In both genomes, trnH1, the gene for tRNA-His(GUG) is located at the extremity of the ...

journal_title：Nucleic acids research

authors： Zurawski G,Bottomley W,Whitfeld PR

更新日期：1984-08-24 00:00:00

abstract：:We have developed an end-labelling approach to map the positions of nucleosomes and protein binding sites at nucleotide resolution by footprinting micrococcal nuclease (MNase)-sensitive sites. Using this approach we determined that the MFA2 gene and its upstream control regions have four positioned nucleosomes when tr...

journal_title：Nucleic acids research

authors： Teng Y,Yu S,Waters R

更新日期：2001-07-01 00:00:00

abstract：:Small RNA (sRNA)-mediated gene silencing phenomena, exemplified by RNA interference (RNAi), require a unique class of proteins called Argonautes (AGOs). An AGO protein typically forms a protein-sRNA complex that contributes to gene silencing using the loaded sRNA as a specificity determinant. Here, we show that MoAGO2...

journal_title：Nucleic acids research

authors： Nguyen Q,Iritani A,Ohkita S,Vu BV,Yokoya K,Matsubara A,Ikeda KI,Suzuki N,Nakayashiki H

更新日期：2018-03-16 00:00:00