COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.

abstract：:RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation....

journal_title：Nucleic acids research

authors： Suresh V,Liu L,Adjeroh D,Zhou X

更新日期：2015-02-18 00:00:00

abstract：:Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribut...

journal_title：Nucleic acids research

authors： Zhang G,Shi J,Zhu S,Lan Y,Xu L,Yuan H,Liao G,Liu X,Zhang Y,Xiao Y,Li X

更新日期：2018-01-04 00:00:00

abstract：:In mammalian cells, DNA damage induces robust changes in gene expression and these changes contribute to the proper execution of cellular responses to DNA damage, including DNA repair, cell cycle arrest and apoptosis. The transcription factor E2F-1 has been suggested to play a key role in the regulation of cell cycle-...

journal_title：Nucleic acids research

authors： Höfferer M,Wirbelauer C,Humar B,Krek W

更新日期：1999-01-15 00:00:00

abstract：:Dlx homeobox genes are first expressed in embryonic retina at E11.5. The Dlx1/Dlx2 null retina has a reduced ganglion cell layer (GCL), with loss of late-born differentiated retinal ganglion cells (RGCs) due to increased apoptosis. TrkB signaling is proposed to regulate the dynamics of RGC apoptosis throughout develop...

journal_title：Nucleic acids research

authors： de Melo J,Zhou QP,Zhang Q,Zhang S,Fonseca M,Wigle JT,Eisenstat DD

更新日期：2008-02-01 00:00:00

abstract：:CLASPIN is an essential mediator in the DNA replication checkpoint, responsible for ATR (ataxia telangiectasia and Rad3-related protein)-dependent activation of CHK1 (checkpoint kinase 1). Here we found a dynamic signaling pathway that regulates CLASPIN turn over. Under unperturbed conditions, the E3 ubiquitin ligase ...

journal_title：Nucleic acids research

authors： Zhu M,Zhao H,Liao J,Xu X

更新日期：2014-12-01 00:00:00

abstract：:A series of plasmids were constructed in which a promoter was introduced into a lac-based operon fusion vector. A perfectly symmetrical oligonucleotide of 22-bp corresponding to an idealized binding site for cAMP receptor protein (CRP) of E. coli was chemically synthesized. The synthetic CRP site was placed between th...

journal_title：Nucleic acids research

authors： Morita T,Shigesada K,Kimizuka F,Aiba H

更新日期：1988-08-11 00:00:00

abstract：:Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A searc...

journal_title：Nucleic acids research

authors： Fouts DE

更新日期：2006-01-01 00:00:00

abstract：:Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must stil...

journal_title：Nucleic acids research

authors： Cox JC,Hayhurst A,Hesselberth J,Bayer TS,Georgiou G,Ellington AD

更新日期：2002-10-15 00:00:00

abstract：:A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and...

journal_title：Nucleic acids research

authors： Isono K

更新日期：1984-01-11 00:00:00

abstract：:The X-ray crystal structure of the complex between the synthetic antitumour and antiviral DNA binding ligand SN 7167 and the DNA oligonucleotide d(CGCGAATTCGCG)2 has been determined to an R factor of 18.3% at 2.6 A resolution. The ligand is located within the minor groove and covers almost 6 bp with the 1-methylpyridi...

journal_title：Nucleic acids research

authors： Squire CJ,Clark GR,Denny WA

更新日期：1997-10-15 00:00:00

abstract：:The antigene strategy based on site-specific recognition of duplex DNA by triplex DNA formation has been exploited in a wide range of biological activities. However, specific triplex formation is mostly restricted to homo-purine strands within the target duplex DNA, due to the destabilizing effect of CG and TA inversi...

journal_title：Nucleic acids research

authors： Wang L,Taniguchi Y,Okamura H,Sasaki S

更新日期：2018-09-28 00:00:00

abstract：:Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarra...

journal_title：Nucleic acids research

authors： Zhao K,Liu M,Burgess RR

更新日期：2010-03-01 00:00:00

abstract：:LTR units associated with cellular retrovirus-like elements are abundantly present in chromosomal DNA of animal cells. We have analyzed the promoter and enhancer activities of diverse LTR units associated with different members of the murine retrovirus-like family known as VL30. We report here that the structurally he...

journal_title：Nucleic acids research

authors： Rotman G,Itin A,Keshet E

更新日期：1986-01-24 00:00:00

abstract：:In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. Ther...

journal_title：Nucleic acids research

authors： Huynh T,Rigoutsos I

更新日期：2004-07-01 00:00:00

abstract：:The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its disc...

journal_title：Nucleic acids research

authors： Silvester N,Alako B,Amid C,Cerdeño-Tárraga A,Cleland I,Gibson R,Goodgame N,Ten Hoopen P,Kay S,Leinonen R,Li W,Liu X,Lopez R,Pakseresht N,Pallreddy S,Plaister S,Radhakrishnan R,Rossello M,Senf A,Smirnov D,Toribio A

更新日期：2015-01-01 00:00:00

abstract：:The high-mobility-group A2 protein (HMGA2) plays important functional roles in transcriptional regulation, DNA replication and chromatin structure. In this study, the effect of histone deacetylase inhibition on the transcriptional activity of the Hmga2 gene was investigated in vivo both at the endogenous gene level an...

journal_title：Nucleic acids research

authors： Ferguson M,Henry PA,Currie RA

更新日期：2003-06-15 00:00:00

abstract：:The macronuclear genome of Euplotes crassus contains two different genes, EFA1 and EFA2, encoding EF-1alpha proteins. They are derived from micronuclear precursors in the course of a sexual process termed conjugation. We have found that two apparent micronuclear precursors exist for EFA1. They differ in their potentia...

journal_title：Nucleic acids research

authors： Florian V,Klein A

更新日期：1996-08-15 00:00:00

abstract：:A filter binding assay was developed that allows measurement of specific binding of trp repressor to operator DNA. The most important feature of this procedure is the concentration and type of salt present in the binding buffer. Using this assay the dissociation constant of the repressor-operator complex was determine...

journal_title：Nucleic acids research

authors： Klig LS,Crawford IP,Yanofsky C

更新日期：1987-07-10 00:00:00

abstract：:We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...

journal_title：Nucleic acids research

authors： Marton A,Delbecchi L,Bourgaux P

更新日期：1991-05-11 00:00:00

abstract：:SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments ...

journal_title：Nucleic acids research

authors： Danilenko M,Dalgliesh C,Pagliarini V,Naro C,Ehrmann I,Feracci M,Kheirollahi-Chadegani M,Tyson-Capper A,Clowry GJ,Fort P,Dominguez C,Sette C,Elliott DJ

更新日期：2017-04-20 00:00:00

abstract：:Labeling of a covalently closed circular double-stranded DNA was achieved using a so-called 'padlock oligonucleotide'. The oligonucleotide was targeted to a sequence which is present in the replication origin of phage f1 and thus in numerous commonly used plasmids. After winding around the double-stranded target DNA s...

journal_title：Nucleic acids research

authors： Roulon T,Coulaud D,Delain E,Le Cam E,Hélène C,Escudé C

更新日期：2002-02-01 00:00:00

abstract：:An improved contact hybridization technique for the analysis of labelled RNA species is presented. The method combines high sensitivity of detection with the high resolution of polyacrylamide gel electrophoresis and should be especially useful for the characterization of transient RNA precursor molecules. Its applicat...

journal_title：Nucleic acids research

authors： Burckhardt J,Telford J,Birnstiel ML

更新日期：1979-07-11 00:00:00

abstract：:We found previously that the Chlamydomonas HSP70A promoter counteracts transcriptional silencing of downstream promoters in a transgene setting. To elucidate the underlying mechanisms, we analyzed chromatin state and transgene expression in transformants containing HSP70A-RBCS2-ble (AR-ble) constructs harboring deleti...

journal_title：Nucleic acids research

authors： Strenkert D,Schmollinger S,Schroda M

更新日期：2013-05-01 00:00:00

abstract：:The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic...

journal_title：Nucleic acids research

authors： Tsai YC,Du D,Domínguez-Malfavón L,Dimastrogiovanni D,Cross J,Callaghan AJ,García-Mena J,Luisi BF

更新日期：2012-11-01 00:00:00

abstract：:The GeneSpeed database (http://genespeed.uchsc.edu/) is an online database and resource tool facilitating the detailed study of protein domain homology in the transcriptomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. The population schema for the GeneSpeed database takes advanta...

journal_title：Nucleic acids research

authors： Kutchma A,Quayum N,Jensen J

更新日期：2007-01-01 00:00:00

abstract：:Bile acid biosynthesis is subjected to feedback regulation whereby bile acids down-regulate their own synthesis. The major point of this regulation is at the level of cholesterol 7alpha-hydroxylase (7alpha-hydroxylase), which controls bile acid output from the classic pathway. This regulation is at the level of transc...

journal_title：Nucleic acids research

authors： del Castillo-Olivares A,Gil G

更新日期：2000-09-15 00:00:00

abstract：:Alfalfa mosaic virus RNA 4, the subgenomic messenger for viral coat protein, was partially digested with RNase T1 or RNase A and the sequence of a number of fragments was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. From overlapping fragments, the complete prima...

journal_title：Nucleic acids research

authors： Brederode FT,Koper-Zwarthoff EC,Bol JF

更新日期：1980-05-24 00:00:00

abstract：:NMR methods were used to investigate a series of mutants of the pseudoknot within the gene 32 messenger RNA of bacteriophage T2, for the purpose of investigating the range of sequences, stem and loop lengths that can form a similar pseudoknot structure. This information is of particular relevance since the T2 pseudokn...

journal_title：Nucleic acids research

authors： Du Z,Hoffman DW

更新日期：1997-03-15 00:00:00

abstract：:Nuclear organization of chromatin is an important level of genome regulation with positional changes of genes occurring during reprogramming. Inherent variability of biological specimens, wide variety of sample preparation and imaging conditions, though pose significant challenges to data analysis and comparison. Here...

journal_title：Nucleic acids research

authors： Jost KL,Haase S,Smeets D,Schrode N,Schmiedel JM,Bertulat B,Herzel H,Cremer M,Cardoso MC

更新日期：2011-09-01 00:00:00

abstract：:The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By sol...

journal_title：Nucleic acids research

authors： Yang J,Jing X,Yi W,Li XD,Yao C,Zhang B,Zheng Z,Wang H,Gong P

更新日期：2021-01-06 00:00:00