ConTra v3: a tool to identify transcription factor binding sites across species, update 2017.

abstract：:To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...

journal_title：Nucleic acids research

authors： Heuchel R,Matthias P,Schaffner W

更新日期：1989-11-25 00:00:00

abstract：:5' strand resection at DNA double strand breaks (DSBs) is critical for homologous recombination (HR) and genomic stability. Here we develop a novel method to quantitatively measure single-stranded DNA intermediates in human cells and find that the 5' strand at endonuclease-generated break sites is resected up to 3.5 k...

journal_title：Nucleic acids research

authors： Zhou Y,Caron P,Legube G,Paull TT

更新日期：2014-02-01 00:00:00

abstract：:The solubility of adult beta-globin chromatin (beta A chromatin) from immature chicken red blood cells can be controlled by the presence or absence of n-butyrate in a cell incubation medium. In the absence of n-butyrate, only a small percentage (approximately 4%) of the total beta A chromatin is in a soluble chromatin...

journal_title：Nucleic acids research

authors： Ferenz CR,Nelson DA

更新日期：1985-03-25 00:00:00

abstract：:MDg3 is a family of mobile dispersed genetic elements represented by 15 copies in the haploid genome of D. melanogaster and flanked, like other similar elements, by the regions of homology. In the present work, these regions of mdg3 have been sequenced. The existence of perfect direct repeats 268 base pairs long has b...

journal_title：Nucleic acids research

authors： Bayev AA Jr,Krayev AS,Lyubomirskaya NV,Ilyin YV,Skryabin KG,Georgiev GP

更新日期：1980-08-11 00:00:00

abstract：:Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...

journal_title：Nucleic acids research

authors： Howes G,O'Connor M,Chia W

更新日期：1988-04-11 00:00:00

abstract：:Lytic infection with polyoma virus leads in Go-arrested primary mouse kidney cell cultures to a mitotic host response. In the present work we focused our attention on cellular RNA synthesis shortly after onset of polyoma T-antigen synthesis. Onset of polyoma-induced stimulation of 45S pre-rRNA synthesis was determined...

journal_title：Nucleic acids research

authors： Matter JM,Tiercy JM,Weil R

更新日期：1983-10-11 00:00:00

abstract：:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silence...

journal_title：Nucleic acids research

authors： Zhu X,Zhang Y,Bjornsdottir G,Liu Z,Quan A,Costanzo M,Dávila López M,Westholm JO,Ronne H,Boone C,Gustafsson CM,Myers LC

更新日期：2011-10-01 00:00:00

abstract：:We describe a new exonuclease-based method for joining and/or constructing two or more DNA molecules. DNA fragments containing ends complementary to those of a vector or another independent molecules were generated by the polymerase chain reaction. The 3' ends of these molecules as well as the vector DNA were then rec...

journal_title：Nucleic acids research

authors： Yang YS,Watson WJ,Tucker PW,Capra JD

更新日期：1993-04-25 00:00:00

abstract：:RNA silencing is an evolutionarily conserved mechanism triggered by double-stranded RNA that is processed into 21- to 24-nt small interfering (si)RNA or micro (mi)RNA by RNaseIII-like enzymes called Dicers. Gene regulations by RNA silencing have fundamental implications in a large number of biological processes that i...

journal_title：Nucleic acids research

authors： Uddin MN,Dunoyer P,Schott G,Akhter S,Shi C,Lucas WJ,Voinnet O,Kim JY

更新日期：2014-07-01 00:00:00

abstract：:A method for the facile preparation of oligoribonucleotide analogues containing beta-d-allofuranosyl nucleosides with additional functional groups tethered to the 6'-O positions is presented. It is based on the synthesis of two protected nucleosides carrying a 6'-O -bromopentyl and a 6'-O -methylaminopentyl substituen...

journal_title：Nucleic acids research

authors： Wu X,Pitsch S

更新日期：1998-10-01 00:00:00

abstract：:We have prepared several novel phosphoramidites and have synthesised oligonucleotides incorporating them internally. The presence of these residues in an oligonucleotide template presents an impossible barrier to primed synthesis by Taq DNA polymerase. When extended as polymerase chain reaction products, these oligonu...

journal_title：Nucleic acids research

authors： Newton CR,Holland D,Heptinstall LE,Hodgson I,Edge MD,Markham AF,McLean MJ

更新日期：1993-03-11 00:00:00

abstract：:Cellular ribonucleic acid (RNA) plays a crucial role in the initial conversion of cellular prion protein PrP(C) to infectious PrP(Sc) or scrapie. The nature of this RNA remains elusive. Previously, RNA aptamers against PrP(C) have been isolated and found to form G-quadruplexes (G4s). PrP(C) binding to G4 RNAs destabil...

journal_title：Nucleic acids research

authors： Olsthoorn RC

更新日期：2014-08-01 00:00:00

abstract：:Several authors, including ourselves, have reported the existence of chromatosomes with DNA size larger than 166 bp in bird erythrocyte chromatin. It was tempting to correlate this increased DNA size with the presence of histone H5. In order to substantiate this hypothesis, we performed a micrococcal nuclease digestio...

journal_title：Nucleic acids research

authors： Muyldermans S,Lasters I,Wyns L,Hamers R

更新日期：1981-08-11 00:00:00

abstract：:The transcriptional activity of a human transposon-like family of repeats, called the THE-1 family, has been studied in cell culture and in human tissue. Both strands of THE-1 are present in several discrete length poly A plus RNAs. Primer extension studies and the structures of cDNA clones show that these THE-1 trans...

journal_title：Nucleic acids research

authors： Paulson KE,Matera AG,Deka N,Schmid CW

更新日期：1987-07-10 00:00:00

abstract：:Flap endonuclease-1 (FEN1) is a member of the Rad2 structure-specific nuclease family. FEN1 possesses FEN, 5'-exonuclease and gap-endonuclease activities. The multiple nuclease activities of FEN1 allow it to participate in numerous DNA metabolic pathways, including Okazaki fragment maturation, stalled replication fork...

journal_title：Nucleic acids research

authors： Zheng L,Jia J,Finger LD,Guo Z,Zer C,Shen B

更新日期：2011-02-01 00:00:00

abstract：:We present the PATHOgenic YEAst Search for Transcriptional Regulators And Consensus Tracking (PathoYeastract - http://pathoyeastract.org) database, a tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in the pathogenic yeasts Candida albicans and C. glabrata Up...

journal_title：Nucleic acids research

authors： Monteiro PT,Pais P,Costa C,Manna S,Sá-Correia I,Teixeira MC

更新日期：2017-01-04 00:00:00

abstract：:The early palindrome domain within the SV40 core origin of replication is essential for the initiation of replication. Studies with single point mutants in this region suggested that the early palindrome domain does not function as a cruciform structure, but may be involved in the initiation of SV40 DNA replication in...

journal_title：Nucleic acids research

authors： Kim YS,Kang HS

更新日期：1989-11-25 00:00:00

abstract：:The purine rich oligodeoxyribonucleotides 1C, d(ATGACGGAATA) and 2C, d(ATGAGCGAATA) alone exhibit highly cooperative melting transitions. Analysis of the concentration dependence of melting, and electrophoretic studies indicate that these oligomers can form an unusual purine rich offset double helix. The unusual duple...

journal_title：Nucleic acids research

authors： Wilson WD,Dotrong MH,Zuo ET,Zon G

更新日期：1988-06-10 00:00:00

abstract：:RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms....

journal_title：Nucleic acids research

authors： Shah A,Chen D,Boda AR,Foster LJ,Davis MJ,Hill MM

更新日期：2015-01-01 00:00:00

abstract：:Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications i...

journal_title：Nucleic acids research

authors： Sterner R,Boffa LC,Chen TA,Allfrey VG

更新日期：1987-06-11 00:00:00

abstract：:Therapeutic small interfering RNAs (siRNAs) are composed of chemically modified nucleotides, which enhance RNA stability and increase affinity in Watson-Crick base pairing. However, the precise fate of such modified nucleotides once the siRNA is degraded within the cell is unknown. Previously, we demonstrated that deo...

journal_title：Nucleic acids research

authors： Wu SY,Chen TM,Gmeiner WH,Chu E,Schmitz JC

更新日期：2013-04-01 00:00:00

abstract：:Topoisomerases (topos) maintain DNA topology and influence DNA transaction processes by catalysing relaxation, supercoiling and decatenation reactions. In the cellular milieu, division of labour between different topos ensures topological homeostasis and control of central processes. In Escherichia coli, DNA gyrase is...

journal_title：Nucleic acids research

authors： Kumar R,Riley JE,Parry D,Bates AD,Nagaraja V

更新日期：2012-11-01 00:00:00

abstract：:This work presents a neutral filter elution method for detecting DNA double strand breaks in mouse L1210 cells after X-ray. The assay will detect the number of double strand breaks induced by as little as 1000 rad of X-ray. The rate of DNA elution through the filters under neutral conditions increases with X-ray dose....

journal_title：Nucleic acids research

authors： Bradley MO,Kohn KW

更新日期：1979-10-10 00:00:00

abstract：:Biological evolution resulted in a homochiral world in which nucleic acids consist exclusively of d-nucleotides and proteins made by ribosomal translation of l-amino acids. From the perspective of synthetic biology, however, particularly anabolic enzymes that could build the mirror-image counterparts of biological mac...

journal_title：Nucleic acids research

authors： Pech A,Achenbach J,Jahnz M,Schülzchen S,Jarosch F,Bordusa F,Klussmann S

更新日期：2017-04-20 00:00:00

abstract：:GenBank(®) (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing proj...

journal_title：Nucleic acids research

authors： Benson DA,Clark K,Karsch-Mizrachi I,Lipman DJ,Ostell J,Sayers EW

更新日期：2015-01-01 00:00:00

abstract：:The circadian clock comprises transcriptional feedback loops of clock genes. Cryptochromes are essential components of the negative feedback loop in mammals as they inhibit CLOCK-BMAL1-mediated transcription. We purified mouse CRY1 (mCRY1) protein complexes from Sarcoma 180 cells to determine their roles in circadian ...

journal_title：Nucleic acids research

authors： Hara Y,Onishi Y,Oishi K,Miyazaki K,Fukamizu A,Ishida N

更新日期：2009-03-01 00:00:00

abstract：:The nucleotide sequences of eight partial and five full-length phaseolin cDNA clones show that phaseolin polypeptides are encoded by two distinct gene families which differ in their coding regions by the presence or absence of two different size direct repeats. The alpha-type phaseolin polypeptides are encoded by gene...

journal_title：Nucleic acids research

authors： Slightom JL,Drong RF,Klassy RC,Hoffman LM

更新日期：1985-09-25 00:00:00

abstract：:The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintai...

journal_title：Nucleic acids research

authors： Grigoriev IV,Nordberg H,Shabalov I,Aerts A,Cantor M,Goodstein D,Kuo A,Minovitsky S,Nikitin R,Ohm RA,Otillar R,Poliakov A,Ratnere I,Riley R,Smirnova T,Rokhsar D,Dubchak I

更新日期：2012-01-01 00:00:00

abstract：:The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequenc...

journal_title：Nucleic acids research

authors： Han A,Kang HJ,Cho Y,Lee S,Kim YJ,Gong S

更新日期：2006-07-01 00:00:00

abstract：:In flowering plants, RNA editing is a posttranscriptional process that converts specific C to U in organelle mRNAs. Nicotiana tabacum is an allotetraploid species derived from the progenitors of Nicotiana sylvestris and Nicotiana tomentosiformis. These Nicotiana species have been used as a model for understanding the ...

journal_title：Nucleic acids research

authors： Okuda K,Habata Y,Kobayashi Y,Shikanai T

更新日期：2008-11-01 00:00:00