The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans.

abstract：:Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

journal_title：Nucleic acids research

authors： Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

更新日期：2013-02-01 00:00:00

abstract：:microRNAs (miRNAs) are small endogenous RNA molecules that are implicated in many biological processes through post-transcriptional regulation of gene expression. The DIANA-microT Web server provides a user-friendly interface for comprehensive computational analysis of miRNA targets in human and mouse. The server has ...

journal_title：Nucleic acids research

authors： Maragkakis M,Vergoulis T,Alexiou P,Reczko M,Plomaritou K,Gousis M,Kourtis K,Koziris N,Dalamagas T,Hatzigeorgiou AG

更新日期：2011-07-01 00:00:00

abstract：:The human beta-actin promoter, including its 5' flanking region and 5' untranslated region, is ubiquitously active in mammalian cells in culture. In this report we investigated the transcriptional activity of, and the protein-DNA interactions that occur within, the proximal region of the human beta-actin promoter. Eff...

journal_title：Nucleic acids research

authors： Danilition SL,Frederickson RM,Taylor CY,Miyamoto NG

更新日期：1991-12-25 00:00:00

abstract：:DNA primer sets, labeled with two fluorescent dyes to exploit fluorescence energy transfer (ET), can be efficiently excited with a single laser line and emit strong fluorescence at distinctive wavelengths. Such ET primers are superior to single fluorophore-labeled primers for DNA sequencing and other multiple color-ba...

journal_title：Nucleic acids research

authors： Ju J,Glazer AN,Mathies RA

更新日期：1996-03-15 00:00:00

abstract：:One of the master regulators of placental cell fusion in mammals leading to multi-nucleated syncytiotrophoblasts is the transcription factor GCMa. Recently, we proved that the cAMP-driven protein kinase A signaling pathway is fundamental for up-regulation of GCMa transcript levels and protein stability. Here, we show ...

journal_title：Nucleic acids research

authors： Schubert SW,Abendroth A,Kilian K,Vogler T,Mayr B,Knerr I,Hashemolhosseini S

更新日期：2008-06-01 00:00:00

abstract：:The yeast protein Rrf1p encoded by the FIL1 nuclear gene bears significant sequence similarity to Escherichia coli ribosome recycling factor (RRF). Here, we call FIL1 Ribosome Recycling Factor of yeast, RRF1. Its gene product, Rrf1p, was localized in mitochondria. Deletion of RRF1 leads to a respiratory incompetent ph...

journal_title：Nucleic acids research

authors： Teyssier E,Hirokawa G,Tretiakova A,Jameson B,Kaji A,Kaji H

更新日期：2003-07-15 00:00:00

abstract：:DNA methylation plays an important role in many biological processes. Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one at a time. Incorporating prior biological inform...

journal_title：Nucleic acids research

authors： Ruan P,Shen J,Santella RM,Zhou S,Wang S

更新日期：2016-09-19 00:00:00

abstract：:Tight cell-cycle regulation of the histone H4-K20 methyltransferase PR-Set7 is essential for the maintenance of genome integrity. In mammals, this mainly involves the interaction of PR-Set7 with the replication factor PCNA, which triggers the degradation of the enzyme by the CRL4CDT2 E3 ubiquitin ligase. PR-Set7 is al...

journal_title：Nucleic acids research

authors： Zouaz A,Fernando C,Perez Y,Sardet C,Julien E,Grimaud C

更新日期：2018-04-06 00:00:00

abstract：:A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the thresh...

journal_title：Nucleic acids research

authors： Scheer M,Klawonn F,Münch R,Grote A,Hiller K,Choi C,Koch I,Schobert M,Härtig E,Klages U,Jahn D

更新日期：2006-07-01 00:00:00

abstract：:We show that in mouse myoblasts the MyoD1 promoter is highly stimulated by MyoD1 expression, suggesting that it is controlled by a positive feedback loop. Using deletion and mutation analyses, we identified the targets for MyoD1 promoter autoregulation as the two proximal E-boxes located close to the MyoD1 core promot...

journal_title：Nucleic acids research

authors： Zingg JM,Pedraza-Alva G,Jost JP

更新日期：1994-06-25 00:00:00

abstract：:In order to examine the nature of the complex formation between the ribosomal protein S1 and nucleic acids three methods were used: Inhibition of the reaction of n-ethyl[2.3 14C]-maleimide with S1 by the addition of oligonucleotides; adsorption of the complexes to nitrocellulose filters; and equilibrium dialysis. The ...

journal_title：Nucleic acids research

authors： Lipecky R,Kohlschein J,Gassen HG

更新日期：1977-10-01 00:00:00

abstract：:The plant gene enod40 is highly conserved among legumes and also present in various non-legume species. It is presumed to play a central regulatory role in the Rhizobium-legume interaction, being expressed well before the initiation of cortical cell divisions resulting in nodule formation. Two small peptides encoded b...

journal_title：Nucleic acids research

authors： Girard G,Roussis A,Gultyaev AP,Pleij CW,Spaink HP

更新日期：2003-09-01 00:00:00

abstract：:The interactions of self-complementary oligonucleotides with a group of metal-mediated DNA-binding drugs, including chromomycin A(3), mithramycin and the novel compound UK-1, were examined via electrospray ionization quadrupole ion trap mass spectrometry. Both chromomycin and mithramycin were shown to bind preferentia...

journal_title：Nucleic acids research

authors： Reyzer ML,Brodbelt JS,Kerwin SM,Kumar D

更新日期：2001-11-01 00:00:00

abstract：:All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first time. As a function of temperature the cytidine amino protons and the imino protons behave very similarly, their relaxatio...

journal_title：Nucleic acids research

authors： Fazakerley GV,van der Marel GA,van Boom JH,Guschlbauer W

更新日期：1984-11-12 00:00:00

abstract：:Translin is a single-stranded RNA- and DNA-binding protein, which has been highly conserved in eukaryotes, from man to Schizosaccharomyces pombe. TRAX is a Translin paralog associated with Translin, which has coevolved with it. We generated structural models of the S. pombe Translin (spTranslin), based on the solved 3...

journal_title：Nucleic acids research

authors： Eliahoo E,Ben Yosef R,Pérez-Cano L,Fernández-Recio J,Glaser F,Manor H

更新日期：2010-05-01 00:00:00

abstract：:Nucleotide excision repair (NER) mechanism is the major pathway responsible for the removal of a large variety of bulky lesions from the genome. Two different NER subpathways have been identified, i.e. the transcription-coupled and the global genome repair pathways. For DNA-damage induced by ultraviolet light both tra...

journal_title：Nucleic acids research

authors： van Oosterwijk MF,Filon R,Kalle WH,Mullenders LH,van Zeeland AA

更新日期：1996-12-01 00:00:00

abstract：:A long-range physical map of the centromeric region of human chromosome 7 has been constructed in order to define the region containing sequences with potential involvement in centromere function. The map is centered around alpha satellite DNA, a family of tandemly repeated DNA forming arrays of hundreds to thousands ...

journal_title：Nucleic acids research

authors： Wevrick R,Willard HF

更新日期：1991-05-11 00:00:00

abstract：:The anaerobically-regulated nirB promoter was used to express heterologous genes in Escherichia coli. Under anaerobic conditions the promoter was able to express tetanus toxin fragment C at approximately 20% total cell protein (tcp) and the Bordetella pertussis antigen pertactin at greater than 30% tcp. These levels a...

journal_title：Nucleic acids research

authors： Oxer MD,Bentley CM,Doyle JG,Peakman TC,Charles IG,Makoff AJ

更新日期：1991-06-11 00:00:00

abstract：:Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and appli...

journal_title：Nucleic acids research

authors： Kuriata A,Gierut AM,Oleniecki T,Ciemny MP,Kolinski A,Kurcinski M,Kmiecik S

更新日期：2018-07-02 00:00:00

abstract：:The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure ...

journal_title：Nucleic acids research

authors： Avraham S,Tung CW,Ilic K,Jaiswal P,Kellogg EA,McCouch S,Pujar A,Reiser L,Rhee SY,Sachs MM,Schaeffer M,Stein L,Stevens P,Vincent L,Zapata F,Ware D

更新日期：2008-01-01 00:00:00

abstract：:The herpes simplex virus protein VP16 interacts with cellular factors, including the protein Oct-1, to activate viral immediate early (IE) gene transcription. We have reproduced this effect by addition of purified, full-length VP16 and the DNA-binding 'POU' domain of Oct-1 (Oct-1/POU) to a HeLa cell in vitro transcrip...

journal_title：Nucleic acids research

authors： Arnosti DN,Preston CM,Hagmann M,Schaffner W,Hope RG,Laughlan G,Luisi BF

更新日期：1993-12-11 00:00:00

abstract：:Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 phi2.5 promoter. Efficient fluorophore labeling of 5' RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current...

journal_title：Nucleic acids research

authors： Li N,Yu C,Huang F

更新日期：2005-02-24 00:00:00

abstract：:Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; howev...

journal_title：Nucleic acids research

authors： Zhou W,Emery SB,Flasch DA,Wang Y,Kwan KY,Kidd JM,Moran JV,Mills RE

更新日期：2020-02-20 00:00:00

abstract：:Human telomerase RNA (hTR) contains several guanine tracts at its 5'-end that can form a G4-quadruplex structure. Previous evidence suggests that a G4-quadruplex within this region disrupts the formation of an important structure within hTR known as the P1 helix, a critical element in defining the template boundary fo...

journal_title：Nucleic acids research

authors： Booy EP,Meier M,Okun N,Novakowski SK,Xiong S,Stetefeld J,McKenna SA

更新日期：2012-05-01 00:00:00

abstract：:Bulky lesions in the template strand block the progression of RNA polymerase II (RNAP II) and are repaired more rapidly than lesions in the non-transcribed strand, which do not block transcription. In order to better understand the basis of this transcription-coupled repair we developed an in vitro system with purifie...

journal_title：Nucleic acids research

authors： Selby CP,Drapkin R,Reinberg D,Sancar A

更新日期：1997-02-15 00:00:00

abstract：:The glycoprotein C (gC) gene of herpes simplex virus type 1 is a true late gene, in that its expression occurs late in infection with a strict requirement for viral DNA replication. Recently, we reported on gC expression during infection with mutant viruses carrying deletions in the gC gene promoter. Analysis of RNA e...

journal_title：Nucleic acids research

authors： Shapira M,Homa FL,Glorioso JC,Levine M

更新日期：1987-04-10 00:00:00

abstract：:We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...

journal_title：Nucleic acids research

authors： Charlier D,Piette J,Glansdorff N

更新日期：1982-10-11 00:00:00

abstract：:Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by...

journal_title：Nucleic acids research

authors： Katz A,Solden L,Zou SB,Navarre WW,Ibba M

更新日期：2014-03-01 00:00:00

abstract：:GC-AG introns represent 0.7% of total human pre-mRNA introns. To study the function of GC-AG introns in splicing regulation, 196 cDNA-confirmed GC-AG introns were identified in Caenorhabditis elegans. These represent 0.6% of the cDNA- confirmed intron data set for this organism. Eleven of these GC-AG introns are invol...

journal_title：Nucleic acids research

authors： Farrer T,Roller AB,Kent WJ,Zahler AM

更新日期：2002-08-01 00:00:00

abstract：:SV40 DNA form I is expressed efficiently after its injection into the nuclei of Xenopus laevis oocytes, resulting in the synthesis of RNA and protein products of both viral late and early transcription units. However it was observed that injection of SV40 genes cloned into pBR322 or related plasmids yielded vastly red...

journal_title：Nucleic acids research

authors： Michaeli T,Prives C

更新日期：1987-02-25 00:00:00