miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.

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 RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry nu...

journal_title：Nucleic acids research

authors： Garavelli JS,Hou Z,Pattabiraman N,Stephens RM

更新日期：2001-01-01 00:00:00

abstract：:Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrates are transpositionally inactive due to the accumulation of mutations in their transposase genes. A novel open reading frame-trapping method was used to isolate uninterrupted transposase coding regions from the genome of the frog s...

journal_title：Nucleic acids research

authors： Miskey C,Izsvák Z,Plasterk RH,Ivics Z

更新日期：2003-12-01 00:00:00

abstract：:Transcriptional repression of pathogen defense-related genes is essential for plant growth and development. Several proteins are known to be involved in the transcriptional regulation of plant defense responses. However, mechanisms by which expression of defense-related genes are regulated by repressor proteins are po...

journal_title：Nucleic acids research

authors： Kim HS,Park HC,Kim KE,Jung MS,Han HJ,Kim SH,Kwon YS,Bahk S,An J,Bae DW,Yun DJ,Kwak SS,Chung WS

更新日期：2012-10-01 00:00:00

abstract：:Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonic...

journal_title：Nucleic acids research

authors： Bottini S,Hamouda-Tekaya N,Tanasa B,Zaragosi LE,Grandjean V,Repetto E,Trabucchi M

更新日期：2017-05-19 00:00:00

abstract：:Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest...

journal_title：Nucleic acids research

authors： Mishra GR,Suresh M,Kumaran K,Kannabiran N,Suresh S,Bala P,Shivakumar K,Anuradha N,Reddy R,Raghavan TM,Menon S,Hanumanthu G,Gupta M,Upendran S,Gupta S,Mahesh M,Jacob B,Mathew P,Chatterjee P,Arun KS,Sharma S,Chand

更新日期：2006-01-01 00:00:00

abstract：:AR9 is a giant Bacillus subtilis phage whose uracil-containing double-stranded DNA genome encodes distant homologs of β and β' subunits of bacterial RNA polymerase (RNAP). The products of these genes are thought to assemble into two non-canonical multisubunit RNAPs - a virion RNAP (vRNAP) that is injected into the hos...

journal_title：Nucleic acids research

authors： Sokolova M,Borukhov S,Lavysh D,Artamonova T,Khodorkovskii M,Severinov K

更新日期：2017-06-02 00:00:00

abstract：:We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...

journal_title：Nucleic acids research

authors： Changchien LM,Craven GR

更新日期：1985-09-11 00:00:00

abstract：:Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a ...

journal_title：Nucleic acids research

authors： Vologodskii AV,Frank-Kamenetskii MD

更新日期：1978-07-01 00:00:00

abstract：:The binary Cre-lox conditional knockout system requires an essential part of the target gene to be flanked by loxP sites, enabling excision in vivo upon Cre expression. LoxP sites are introduced by homologous recombination, together with a selectable marker. However, this marker can disturb gene expression and should ...

journal_title：Nucleic acids research

authors： Leneuve P,Colnot S,Hamard G,Francis F,Niwa-Kawakita M,Giovannini M,Holzenberger M

更新日期：2003-03-01 00:00:00

abstract：:With the aid of a novel poly-dA tailing-partial restriction technique and S1-protection mapping, the 5' terminal coding sequence for the 40S precursor ribosomal RNA of Xenopus laevis has been exactly identified. Since the promoter sequence for the 40S RNA should lie close to its 5' terminal coding sequence, we are abl...

journal_title：Nucleic acids research

authors： Moss T,Birnstiel ML

更新日期：1979-08-24 00:00:00

abstract：:The antitumour antibiotics bleomycin and actinomycin are commonly used therapeutically in combination. One causes metal ion- and oxygen-dependent oxidative damage to DNA, while the other acts at the level of DNA via intercalation of its phenoxazone chromophore and probable inhibition of topoisomerases. Both drugs bind...

journal_title：Nucleic acids research

authors： Bailly C,Kénani A,Waring MJ

更新日期：1997-04-15 00:00:00

abstract：:Properties of a mutant bacteriophage T2 DNA [N:(6)-adenine] methyltransferase (T2 Dam MTase) have been investigated for its potential utilization in RecA-assisted restriction endonuclease (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type T4 Dam, both wild...

journal_title：Nucleic acids research

authors： Minko I,Hattman S,Lloyd RS,Kossykh V

更新日期：2001-04-01 00:00:00

abstract：:Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets with a methyl thioether group (-SCH(3)). Members of two of the four known subgroups of MTTases...

journal_title：Nucleic acids research

authors： Anton BP,Russell SP,Vertrees J,Kasif S,Raleigh EA,Limbach PA,Roberts RJ

更新日期：2010-10-01 00:00:00

abstract：:To generate long arrays of nucleosomes within a topologically defined chromatin domain we have assembled minichromosomes on negatively supercoiled plasmid DNA with extracts from Drosophila preblastoderm embryos. These minichromosomes are dynamic substrates for energy-dependent nucleosome remodeling machines that facil...

journal_title：Nucleic acids research

authors： Venditti P,Di Croce L,Kauer M,Blank T,Becker PB,Beato M

更新日期：1998-08-15 00:00:00

abstract：:The selective and potent inhibition of mitochondrial translation in Saccharomyces cerevisiae by pentamidine suggests a novel antimicrobial action for this drug. Electrophoresis mobility shift assay, T1 ribonuclease footprinting, hydroxyl radical footprinting and isothermal titration calorimetry collectively demonstrat...

journal_title：Nucleic acids research

authors： Sun T,Zhang Y

更新日期：2008-03-01 00:00:00

abstract：:A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...

journal_title：Nucleic acids research

authors： Cui L,Fan Q,Li J

更新日期：2002-11-01 00:00:00

abstract：:The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regula...

journal_title：Nucleic acids research

authors： Gong F,Sun L,Wang Z,Shi J,Li W,Wang S,Han X,Sun Y

更新日期：2011-06-01 00:00:00

abstract：:The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...

journal_title：Nucleic acids research

authors： Cullen D,Wilson LJ,Grey GL,Henner DJ,Turner G,Ballance DJ

更新日期：1987-11-25 00:00:00

abstract：:Phage display technology involves the display of proteins or peptides, as coat protein fusions, on the surface of a phage or phagemid particles. Using standard technology, helper phage are essential for the replication and assembly of phagemid particles, during library production and biopanning. We have eliminated the...

journal_title：Nucleic acids research

authors： Chasteen L,Ayriss J,Pavlik P,Bradbury AR

更新日期：2006-01-01 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：:Cancer-associated somatic mutations outside protein-coding regions remain largely unexplored. Analyses of the TERT locus have indicated that non-coding regulatory mutations can be more frequent than previously suspected and play important roles in oncogenesis. Using a computational method called SASE-hunter, developed...

journal_title：Nucleic acids research

authors： Smith KS,Yadav VK,Pedersen BS,Shaknovich R,Geraci MW,Pollard KS,De S

更新日期：2015-06-23 00:00:00

abstract：:This review takes a second look at a set of mRNAs that purportedly employ an alternative mechanism of initiation when cap-dependent translation is reduced during mitosis or stress conditions. A closer look is necessary because evidence cited in support of the internal initiation hypothesis is often flawed. When putati...

journal_title：Nucleic acids research

authors： Kozak M

更新日期：2005-11-28 00:00:00

abstract：:We recently identified a region of preferential replication initiation, oriGNAI3, near the 3' end of the Chinese hamster GNAI3 gene. oriGNAI3 is co-amplified in mutants selected for AMPD2 amplification, a process generating chromosomal rearrangements. In this report we have taken advantage of cell lines with truncated...

journal_title：Nucleic acids research

authors： Toledo F,Lachagès AM,Mayau V,Debatisse M

更新日期：1999-04-01 00:00:00

abstract：:The advent of RNA-sequencing and microarray technologies has led to rapid growth of transcriptome data generated for a wide range of organisms, under various cellular, organ and individual conditions. Since the number of possible combinations of intercellular and extracellular conditions is almost unlimited, catalogin...

journal_title：Nucleic acids research

authors： Obayashi T,Kagaya Y,Aoki Y,Tadaka S,Kinoshita K

更新日期：2019-01-08 00:00:00

abstract：:Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and ...

journal_title：Nucleic acids research

authors： Yu NY,Hallström BM,Fagerberg L,Ponten F,Kawaji H,Carninci P,Forrest AR,Fantom Consortium.,Hayashizaki Y,Uhlén M,Daub CO

更新日期：2015-08-18 00:00:00

abstract：:The hypothesis that DNA strands complementary to the coding strand contain in phase coding sequences has been investigated. Statistical analysis of the 50 genes of bacteriophage T7 shows no significant correlation between patterns of codon usage on the coding and non-coding strands. In Bacillus and yeast genes the cor...

journal_title：Nucleic acids research

authors： Sharp PM

更新日期：1985-02-25 00:00:00

abstract：:NRPS-PKS is web-based software for analysing large multi-enzymatic, multi-domain megasynthases that are involved in the biosynthesis of pharmaceutically important natural products such as cyclosporin, rifamycin and erythromycin. NRPS-PKS has been developed based on a comprehensive analysis of the sequence and structur...

journal_title：Nucleic acids research

authors： Ansari MZ,Yadav G,Gokhale RS,Mohanty D

更新日期：2004-07-01 00:00:00

abstract：:The vitamin D receptor mediates the signal of 1 alpha, 25-dihydroxyvitamin D3 by binding to vitamin D responsive elements in DNA as a homodimer or as a heterodimer composed of one vitamin D receptor subunit and one retinoid X receptor subunit. We have mapped the dimerization interfaces of the vitamin D receptor that i...

journal_title：Nucleic acids research

authors： Nishikawa J,Kitaura M,Imagawa M,Nishihara T

更新日期：1995-02-25 00:00:00

abstract：:Pre-mRNA transcripts in a variety of organisms, including plants, Drosophila and Caenorhabditis elegans, contain introns which are significantly richer in adenosine and uridine residues than their flanking exons. Previous analyses using exonic and intronic replacements between two nonequivalent 5'splice sites in the 4...

journal_title：Nucleic acids research

authors： McCullough AJ,Schuler MA

更新日期：1997-03-01 00:00:00