FlyBase at 25: looking to the future.

abstract：:Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs ...

journal_title：Nucleic acids research

authors： Li JT,Zhang Y,Kong L,Liu QR,Wei L

更新日期：2008-09-01 00:00:00

abstract：:Upon HIV-1 infection of a target cell, the viral reverse transcriptase (RT) copies the genomic RNA to synthesize the viral DNA. The genomic RNA is within the incoming HIV-1 core where it is coated by molecules of nucleocapsid (NC) protein that chaperones the reverse transcription process. Indeed, the RT chaperoning pr...

journal_title：Nucleic acids research

authors： Grigorov B,Bocquin A,Gabus C,Avilov S,Mély Y,Agopian A,Divita G,Gottikh M,Witvrouw M,Darlix JL

更新日期：2011-07-01 00:00:00

abstract：:Reactive oxygen species produced by endogenous metabolic activity and exposure to a multitude of exogenous agents impact cells in a variety of ways. The DNA base damage 8-oxodeoxyguanosine (8-oxodG) is a prominent indicator of oxidative stress and has been well-characterized as a premutagenic lesion in mammalian cells...

journal_title：Nucleic acids research

authors： Ghosh R,Mitchell DL

更新日期：1999-08-01 00:00:00

abstract：:Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...

journal_title：Nucleic acids research

authors： Chung CZ,Jaramillo JE,Ellis MJ,Bour DYN,Seidl LE,Jo DHS,Turk MA,Mann MR,Bi Y,Haniford DB,Duennwald ML,Heinemann IU

更新日期：2019-04-08 00:00:00

abstract：:Every bulky lesion in DNA can potentially inhibit the Taq DNA polymerase and thereby decrease the amplification produced in the polymerase chain reaction. We investigated the feasibility of using this inhibition to quantify DNA lesions produced by the anticancer drug cisplatin. Products were detected by electrophoresi...

journal_title：Nucleic acids research

authors： Jennerwein MM,Eastman A

更新日期：1991-11-25 00:00:00

abstract：:Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and transla...

journal_title：Nucleic acids research

authors： Krishna SS,Majumdar I,Grishin NV

更新日期：2003-01-15 00:00:00

abstract：:Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3'UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism...

journal_title：Nucleic acids research

authors： Takeuchi A,Schmitt D,Chapple C,Babaylova E,Karpova G,Guigo R,Krol A,Allmang C

更新日期：2009-04-01 00:00:00

abstract：:DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been dev...

journal_title：Nucleic acids research

authors： Fili N,Mashanov GI,Toseland CP,Batters C,Wallace MI,Yeeles JT,Dillingham MS,Webb MR,Molloy JE

更新日期：2010-07-01 00:00:00

abstract：:TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully cha...

journal_title：Nucleic acids research

authors： McKerlie M,Walker JR,Mitchell TR,Wilson FR,Zhu XD

更新日期：2013-12-01 00:00:00

abstract：:Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assum...

journal_title：Nucleic acids research

authors： Liljeström PL,Liljeström P

更新日期：1987-03-11 00:00:00

abstract：:The homeobox-containing gene Hex is expressed in several cell types, including thyroid follicular cells, in which it regulates the transcription of tissue- specific genes. In this study the regulation of Hex promoter activity was investigated. Using co- transfection experiments, we demonstrated that the transcriptiona...

journal_title：Nucleic acids research

authors： Puppin C,D'Elia AV,Pellizzari L,Russo D,Arturi F,Presta I,Filetti S,Bogue CW,Denson LA,Damante G

更新日期：2003-04-01 00:00:00

abstract：:Comparative analysis of mutants using transfection is complicated by clones exhibiting variable levels of gene expression due to copy number differences and genomic position effects. Recombinase-mediated cassette exchange (RMCE) can overcome these problems by introducing the target gene into pre-determined chromosomal...

journal_title：Nucleic acids research

authors： Wong ET,Kolman JL,Li YC,Mesner LD,Hillen W,Berens C,Wahl GM

更新日期：2005-10-04 00:00:00

abstract：:The genome stability is maintained by coordinated action of DNA repairs and checkpoints, which delay progression through the cell cycle in response to DNA damage. Rad9 is conserved from yeast to human and functions in cell cycle checkpoint controls. Here, a regulatory mechanism for Rad9 function is reported. In this s...

journal_title：Nucleic acids research

authors： He W,Ma X,Yang X,Zhao Y,Qiu J,Hang H

更新日期：2011-06-01 00:00:00

abstract：:Increasing experimental evidence shows a prominent role of histone modifications in the coordinated control of gene expression in the human malaria parasite Plasmodium falciparum. The search for the histone-mark-reading machinery that translates histone modifications into biological processes, such as formation of het...

journal_title：Nucleic acids research

authors： Pérez-Toledo K,Rojas-Meza AP,Mancio-Silva L,Hernández-Cuevas NA,Delgadillo DM,Vargas M,Martínez-Calvillo S,Scherf A,Hernandez-Rivas R

更新日期：2009-05-01 00:00:00

abstract：:Using a bio-oligo pull-down DNA-binding assay we investigated the binding capacity of endogenous, DNA damage-induced p53 in human diploid fibroblasts to several p53-responsive elements (REs) present in p53-regulated genes. During the course of p53 accumulation, we observed a decrease in p53 binding to the GADD45 but n...

journal_title：Nucleic acids research

authors： Buzek J,Latonen L,Kurki S,Peltonen K,Laiho M

更新日期：2002-06-01 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：:Synthetic deoxyoligonucleotides have been 5'-aminoalkylated at the end of step-wise synthesis on the polymer support. This was achieved through the activation of the 5'-hydroxyl group as its 5'-imidazolyl derivative using carbonyldiimidazole, which was subsequently displaced with hexamethylene diamine to yield the tit...

journal_title：Nucleic acids research

authors： Wachter L,Jablonski JA,Ramachandran KL

更新日期：1986-10-24 00:00:00

abstract：:We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...

journal_title：Nucleic acids research

authors： Del Villar-Guerra R,Gray RD,Trent JO,Chaires JB

更新日期：2018-04-20 00:00:00

abstract：:The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...

journal_title：Nucleic acids research

authors： Zhu QS,Heisterkamp N,Groffen J

更新日期：1990-12-11 00:00:00

abstract：:GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data. This bias can dominate the signal of interest for analyses that focus on measuring fragment abundance within a genome, such as copy number estimation (DNA-seq). The bias is not consistent b...

journal_title：Nucleic acids research

authors： Benjamini Y,Speed TP

更新日期：2012-05-01 00:00:00

abstract：:Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction Of M8G into DNA sequences markedly stabilizes the Z conformation under low salt conditions. The hexamer d(CGC[M8G]CG)2 exhibits a CD spectrum characteristic of th...

journal_title：Nucleic acids research

authors： Sugiyama H,Kawai K,Matsunaga A,Fujimoto K,Saito I,Robinson H,Wang AH

更新日期：1996-04-01 00:00:00

abstract：:Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which ...

journal_title：Nucleic acids research

authors： Dai M,Wang P,Boyd AD,Kostov G,Athey B,Jones EG,Bunney WE,Myers RM,Speed TP,Akil H,Watson SJ,Meng F

更新日期：2005-11-10 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：:The androgen receptor (AR) is a member of the nuclear hormone receptor family of transcription factors that plays a critical role in regulating expression of genes involved in prostate development and transformation. Upon hormone binding, the AR associates with numerous co-regulator proteins that regulate the activati...

journal_title：Nucleic acids research

authors： Gaughan L,Stockley J,Wang N,McCracken SR,Treumann A,Armstrong K,Shaheen F,Watt K,McEwan IJ,Wang C,Pestell RG,Robson CN

更新日期：2011-03-01 00:00:00

abstract：:In squid (Loligo bleekeri) mitochondria, the two 3'-terminal nucleotides (G72-G73) of the tRNA(Tyr) gene overlap with the two 5'-terminal nucleotides (G1-G2) of the downstream tRNA(Cys) gene. To elucidate the processing mechanism(s) of the tRNA molecules derived from this region, tRNAs were analyzed by sequencing cDNA...

journal_title：Nucleic acids research

authors： Tomita K,Ueda T,Watanabe K

更新日期：1996-12-15 00:00:00

abstract：:Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific nucleases such as Transcription Activator-Like Effectors Nucleases (TALENs) and Cas9-gRNA allows...

journal_title：Nucleic acids research

authors： Yang L,Guell M,Byrne S,Yang JL,De Los Angeles A,Mali P,Aach J,Kim-Kiselak C,Briggs AW,Rios X,Huang PY,Daley G,Church G

更新日期：2013-10-01 00:00:00

abstract：:The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the...

journal_title：Nucleic acids research

authors： Federhen S

更新日期：2012-01-01 00:00:00

abstract：:The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is ...

journal_title：Nucleic acids research

authors： Kayala MA,Baldi P

更新日期：2012-07-01 00:00:00

abstract：:Interactions between subunits in the Saccharomyces cerevisiae ribosome are mediated by universal and eukaryote-specific intersubunit bridges. Universal bridges are positioned close to the ribosomal functional centers, while eukaryote-specific bridges are mainly located on the periphery of the ribosome. Two bridges, eB...

journal_title：Nucleic acids research

authors： Kisly I,Remme J,Tamm T

更新日期：2019-01-10 00:00:00

abstract：UNLABELLED:The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have im...

journal_title：Nucleic acids research

authors： Gijón-Correas JA,Andrade-Navarro MA,Fontaine JF

更新日期：2014-07-01 00:00:00