WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families.

abstract：:We report that greA expression is driven by two strong, overlapping P1 and P2 promoters. The P1 promoter is sigma(70)-dependent and P2 is sigma(E)-dependent. Two-thirds of transcripts terminate within the leader region and the remaining third comprises greA mRNA. Termination efficiency seems to be unaffected by growth...

journal_title：Nucleic acids research

authors： Potrykus K,Murphy H,Chen X,Epstein JA,Cashel M

更新日期：2010-03-01 00:00:00

abstract：:We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist t...

journal_title：Nucleic acids research

authors： Mytelka DS,Chamberlin MJ

更新日期：1996-07-15 00:00:00

abstract：:In plants, nuclear multisubunit RNA polymerases IV and V are RNA Polymerase II-related enzymes that synthesize non-coding RNAs for RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Here, we tested the importance of the C-terminal domain (CTD) of Pol IV's largest subunit given that the Pol II CTD ...

journal_title：Nucleic acids research

authors： Wendte JM,Haag JR,Pontes OM,Singh J,Metcalf S,Pikaard CS

更新日期：2019-09-26 00:00:00

abstract：:We report the consensus sequence of members of a new dispersed middle-repetitive DNA family, MT, which is present in mouse and rat genomes. This family is shown to be as abundant as the described rodent B1 and B2 families. Hybridization experiments with radioactive single-stranded cDNAs from different tissues indicate...

journal_title：Nucleic acids research

authors： Heinlein UA,Lange-Sablitzky R,Schaal H,Wille W

更新日期：1986-08-26 00:00:00

abstract：:Benzo[c]phenanthrene dihydrodiol epoxide (B[c] PhDE) is well known as an important environmental chemical carcinogen that preferentially modifies DNA in adenine residues. However, the molecular mechanism by which B[c]PhDE induces tumorigenesis is not fully understood. In this report, we demonstrate that DNA mismatch r...

journal_title：Nucleic acids research

authors： Wu J,Zhu BB,Yu J,Zhu H,Qiu L,Kindy MS,Gu L,Seidel A,Li GM

更新日期：2003-11-15 00:00:00

abstract：:MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we hav...

journal_title：Nucleic acids research

authors： Gabriels R,Martens L,Degroeve S

更新日期：2019-07-02 00:00:00

abstract：:PAX6 is a transcription factor that plays a major role in ocular morphogenesis. PAX6 is expressed in the eye, central nervous system and pancreas. Two alternative promoters, P0 and P1, which are differentially regulated during development, drive PAX6 transcription. We identified a 57 bp cis-regulatory element in exon ...

journal_title：Nucleic acids research

authors： Zheng JB,Zhou YH,Maity T,Liao WS,Saunders GF

更新日期：2001-10-01 00:00:00

abstract：:We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...

journal_title：Nucleic acids research

authors： Hochleitner K,Thomale J,Nikitin AYu,Rajewsky MF

更新日期：1991-08-25 00:00:00

abstract：:ATF4 is a pro-oncogenic transcription factor whose translation is activated by eIF2 phosphorylation through delayed re-initiation involving two uORFs in the mRNA leader. However, in yeast, the effect of eIF2 phosphorylation can be mimicked by eIF5 overexpression, which turns eIF5 into translational inhibitor, thereby ...

journal_title：Nucleic acids research

authors： Kozel C,Thompson B,Hustak S,Moore C,Nakashima A,Singh CR,Reid M,Cox C,Papadopoulos E,Luna RE,Anderson A,Tagami H,Hiraishi H,Slone EA,Yoshino KI,Asano M,Gillaspie S,Nietfeld J,Perchellet JP,Rothenburg S,Masai H,W

更新日期：2016-10-14 00:00:00

abstract：:The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for N...

journal_title：Nucleic acids research

authors： Wells CD,Deighan P,Brigham M,Hochschild A

更新日期：2016-06-20 00:00:00

abstract：:Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unus...

journal_title：Nucleic acids research

authors： Riazuddin S,Athar A,Sohail A

更新日期：1987-11-25 00:00:00

abstract：:VA RNA(I) is a non-coding adenoviral transcript that counteracts the host cell anti-viral defenses such as immune responses mediated via PKR. We investigated potential alternate secondary structure conformations within the PKR-binding domain of VA RNA(I) using site-directed mutagenesis, RNA UV-melting analysis and enz...

journal_title：Nucleic acids research

authors： Wahid AM,Coventry VK,Conn GL

更新日期：2009-09-01 00:00:00

abstract：:Eucaryotic transcription initiation by RNA polymerase II involves protein:DNA interactions during the formation of a transcription complex. In addition to RNA polymerase II there are at least five other general transcription factors necessary for initiation with the adenovirus major late promoter. One of these, TFIIA,...

journal_title：Nucleic acids research

authors： Burke C,Yu XB,Marchitelli L,Davis EA,Ackerman S

更新日期：1990-06-25 00:00:00

abstract：:The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of no...

journal_title：Nucleic acids research

authors： Grosjean H,Westhof E

更新日期：2016-09-30 00:00:00

abstract：:BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along ...

journal_title：Nucleic acids research

authors： Dai HJ,Huang CH,Lin RT,Tsai RT,Hsu WL

更新日期：2008-07-01 00:00:00

abstract：:FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...

journal_title：Nucleic acids research

authors： Cock PJ,Fields CJ,Goto N,Heuer ML,Rice PM

更新日期：2010-04-01 00:00:00

abstract：:Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2, which functions in mRNA biogenesis and export. Here, we investigate th...

journal_title：Nucleic acids research

authors： García-Oliver E,Pascual-García P,García-Molinero V,Lenstra TL,Holstege FC,Rodríguez-Navarro S

更新日期：2013-06-01 00:00:00

abstract：:The vertebrate genome is a mosaic of regions differing dramatically in their G + C content. Those regions with a high G + C content contain the expected number of CpG dinucleotides and we propose that following methylation these have been protected from deamination by the increased stability of the surrounding DNA dup...

journal_title：Nucleic acids research

authors： Adams RL,Eason R

更新日期：1984-07-25 00:00:00

abstract：:Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interact...

journal_title：Nucleic acids research

authors： Fuchs A,Riegler S,Ayatollahi Z,Cavallari N,Giono LE,Nimeth BA,Mutanwad KV,Schweighofer A,Lucyshyn D,Barta A,Petrillo E,Kalyna M

更新日期：2021-01-25 00:00:00

abstract：:Oligodeoxyribonucleotides containing N4-methoxycytosine (mo4C), N4-methoxy-5-methylcytosine (mo4m5C) and other base-analogues were synthesised and used to compare the stabilities of duplexes containing mo4C.A and mo4C.G base pairs with those containing normal and mismatch pairs. The Tm values and other thermodynamic p...

journal_title：Nucleic acids research

authors： Anand NN,Brown DM,Salisbury SA

更新日期：1987-10-26 00:00:00

abstract：:Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux-Apache-MySQL-PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by b...

journal_title：Nucleic acids research

authors： Chen SH,Lin CY,Cho CS,Lo CZ,Hsiung CA

更新日期：2003-07-01 00:00:00

abstract：:Genome organization into transcriptionally active domains denotes one of the first levels of gene expression regulation. Although the chromatin domain concept is generally accepted, only little is known on how domain organization impacts the regulation of differential gene expression. Insulators might hold answers to ...

journal_title：Nucleic acids research

authors： Furlan-Magaril M,Rebollar E,Guerrero G,Fernández A,Moltó E,González-Buendía E,Cantero M,Montoliu L,Recillas-Targa F

更新日期：2011-01-01 00:00:00

abstract：:Mouse DNA contains two equally abundant, homologous subfamilies of MspI 3.6 and 5 kb repeated fragments. The first subfamily corresponds to the previously described (1) Bam 4 kb repeats, the second one to Bam repeated fragments of higher molecular weight. These subfamilies account for the vast majority of long Bam rep...

journal_title：Nucleic acids research

authors： Meunier-Rotival M,Bernardi G

更新日期：1984-02-10 00:00:00

abstract：:The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 ...

journal_title：Nucleic acids research

authors： Frykholm K,Berntsson RP,Claesson M,de Battice L,Odegrip R,Stenmark P,Westerlund F

更新日期：2016-09-06 00:00:00

abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...

journal_title：Nucleic acids research

authors： Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JA

更新日期：2007-01-01 00:00:00

abstract：:We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the ...

journal_title：Nucleic acids research

authors： Ning S,Yue M,Wang P,Liu Y,Zhi H,Zhang Y,Zhang J,Gao Y,Guo M,Zhou D,Li X,Li X

更新日期：2017-01-04 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：:IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...

journal_title：Nucleic acids research

authors： Shi L,Qiu D,Zhao G,Corthesy B,Lees-Miller S,Reeves WH,Kao PN

更新日期：2007-01-01 00:00:00

abstract：:PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tool...

journal_title：Nucleic acids research

authors： Duvick J,Fu A,Muppirala U,Sabharwal M,Wilkerson MD,Lawrence CJ,Lushbough C,Brendel V

更新日期：2008-01-01 00:00:00

abstract：:Previous studies have established a critical role of both TFIIB and RNA polymerase II (RNAPII) in start site selection in the yeast Saccharomyces cerevisiae. However, it remains unclear how the TFIIB-RNAPII interaction impacts on this process since such an interaction can potentially influence both preinitiation compl...

journal_title：Nucleic acids research

authors： Zhang DY,Carson DJ,Ma J

更新日期：2002-07-15 00:00:00