Differential regulation of RNF8-mediated Lys48- and Lys63-based poly-ubiquitylation.

abstract：:Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep)...

journal_title：Nucleic acids research

authors： Pastrana CL,Carrasco C,Akhtar P,Leuba SH,Khan SA,Moreno-Herrero F

更新日期：2016-10-14 00:00:00

abstract：:The swi4+ gene of Schizosaccharomyces pombe is involved in termination of copy-synthesis during mating-type switching. The gene was cloned by functional complementation of a swi4 mutant transformed with a genomic library. Determination of the nucleotide sequence revealed an open reading frame of 2979 nucleotides which...

journal_title：Nucleic acids research

authors： Fleck O,Michael H,Heim L

更新日期：1992-05-11 00:00:00

abstract：:Transcription of 5S RNA gene in Xenopus oocytes requires a 38 kDa transcription factor TFIIIA, which interacts with the 50 bp internal control region of the gene. We looked for TFIIIA-like polypeptides in the extracts of adult Xenopus tissues on the basis of their antigenic cross-reactivity to anti-TFIIIA antibody. Se...

journal_title：Nucleic acids research

authors： Yasui W,Ryoji M

更新日期：1989-07-25 00:00:00

abstract：:Transgenic mice suitable for the in vivo assay of suspected mutagens at the chromosome level have been constructed by stable integration of a lambda phage shuttle vector. The shuttle vector, which contains a beta-galactosidase (beta-gal) target gene, can be rescued from genomic DNA with in vitro packaging extracts. Mu...

journal_title：Nucleic acids research

authors： Kohler SW,Provost GS,Kretz PL,Dycaico MJ,Sorge JA,Short JM

更新日期：1990-05-25 00:00:00

abstract：:The three dimensional structures for representatives of nearly half of all protein families are now available in public databases. Thus, no matter which protein one investigates, it is increasingly likely that the 3D structure of a homolog will be known and may reveal unsuspected structure-function relationships. The ...

journal_title：Nucleic acids research

authors： Marchler-Bauer A,Addess KJ,Chappey C,Geer L,Madej T,Matsuo Y,Wang Y,Bryant SH

更新日期：1999-01-01 00:00:00

abstract：:Protein-protein interactions regulate many essential enzymatic processes in the cell. Somatic mutations outside of an enzyme active site can therefore impact cellular function by disruption of critical protein-protein interactions. In our investigation of the cellular impact of the T304I cancer mutation of DNA Polymer...

journal_title：Nucleic acids research

authors： Fang Q,Andrews J,Sharma N,Wilk A,Clark J,Slyskova J,Koczor CA,Lans H,Prakash A,Sobol RW

更新日期：2019-07-09 00:00:00

abstract：:Prior work has indicated that an octanucleotide [5'TATAAGTA(+1)3'] sequence is used as a promoter in yeast mitochondria. Two such sequences (FP1 and FP2) are present upstream of the tRNA(fMet)-RNAse P RNA -tRNA(Pro) gene cluster but only the FP1 promoter but not the FP2 appears to be active in vivo and in vitro. The r...

journal_title：Nucleic acids research

authors： Biswas TK

更新日期：1991-11-11 00:00:00

abstract：:The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first f...

journal_title：Nucleic acids research

authors： Lo YS,Lin CY,Yang JM

更新日期：2010-07-01 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：:In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant propo...

journal_title：Nucleic acids research

authors： Tsirigos A,Rigoutsos I

更新日期：2005-02-16 00:00:00

abstract：:Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...

journal_title：Nucleic acids research

authors： Margraf T,Schenk G,Torda AE

更新日期：2009-07-01 00:00:00

abstract：:Muscle creatine kinase (MCK) is a major enzyme of cellular energy metabolism that is expressed upon differentiation of myoblasts into myotubes. Previously we cloned and sequenced the entire rabbit enzyme cDNA which was used as a probe in these studies to obtain a genomic clone from a rabbit library. The transcription ...

journal_title：Nucleic acids research

authors： Yi TM,Walsh K,Schimmel P

更新日期：1991-06-11 00:00:00

abstract：:Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidop...

journal_title：Nucleic acids research

authors： Ziolkowski PA,Koczyk G,Galganski L,Sadowski J

更新日期：2009-06-01 00:00:00

abstract：:Helicase-nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. Here we show that HerA...

journal_title：Nucleic acids research

authors： Blackwood JK,Rzechorzek NJ,Abrams AS,Maman JD,Pellegrini L,Robinson NP

更新日期：2012-04-01 00:00:00

abstract：:Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in ...

journal_title：Nucleic acids research

authors： Popenda M,Milecki J,Adamiak RW

更新日期：2004-08-03 00:00:00

abstract：:We describe the structure (3840 bp) of a novel Euglena gracilis chloroplast ribosomal protein operon that encodes the five genes rpl16-rpl14-rpl5-rps8-rpl36. The gene organization resembles the spc and the 3'-end of the S10 ribosomal protein operons of E. coli. The rpl5 is a new chloroplast gene not previously reporte...

journal_title：Nucleic acids research

authors： Christopher DA,Hallick RB

更新日期：1989-10-11 00:00:00

abstract：:The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...

journal_title：Nucleic acids research

authors： Maheswari U,Mock T,Armbrust EV,Bowler C

更新日期：2009-01-01 00:00:00

abstract：:The DEAH-box NTPase Prp43 disassembles spliceosomes in co-operation with the cofactors Ntr1/Spp382 and Ntr2, forming the NTR complex. How Prp43 is regulated by its cofactors to discard selectively only intron-lariat spliceosomes (ILS) and defective spliceosomes and to prevent disassembly of earlier and properly assemb...

journal_title：Nucleic acids research

authors： Fourmann JB,Tauchert MJ,Ficner R,Fabrizio P,Lührmann R

更新日期：2017-04-20 00:00:00

abstract：:Loss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage re...

journal_title：Nucleic acids research

authors： Jarrett SG,Wolf Horrell EM,D'Orazio JA

更新日期：2016-12-15 00:00:00

abstract：:Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase acti...

journal_title：Nucleic acids research

authors： Ristic D,Modesti M,van der Heijden T,van Noort J,Dekker C,Kanaar R,Wyman C

更新日期：2005-06-08 00:00:00

abstract：:An oligodeoxyribonucleotide, d(GCTCACAAT-X-ATTGTGAGC), where X represents a hexaethylene glycol chain, was studied using circular dichroism spectroscopy. Its conformation and conformational stability were compared to those of compounds where X was replaced by four thymines and to the duplex of same sequence without lo...

journal_title：Nucleic acids research

authors： Durand M,Chevrie K,Chassignol M,Thuong NT,Maurizot JC

更新日期：1990-11-11 00:00:00

abstract：:Poly (ADP-ribose) polymerase 1 (PARP1) has emerged as an attractive target for cancer therapy due to its key role in DNA repair processes. Inhibition of PARP1 in BRCA-mutated cancers has been observed to be clinically beneficial. Recent genome-mapping experiments have identified a non-canonical G-quadruplex-forming se...

journal_title：Nucleic acids research

authors： Sengar A,Vandana JJ,Chambers VS,Di Antonio M,Winnerdy FR,Balasubramanian S,Phan AT

更新日期：2019-02-20 00:00:00

abstract：:Controller (C) proteins regulate the timing of the expression of restriction and modification (R-M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene and the endonuclease gene; at higher concentrations, a second dimer bo...

journal_title：Nucleic acids research

authors： McGeehan JE,Streeter SD,Thresh SJ,Ball N,Ravelli RB,Kneale GG

更新日期：2008-08-01 00:00:00

abstract：:Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...

journal_title：Nucleic acids research

authors： Sen GC,Ghosh HP

更新日期：1976-03-01 00:00:00

abstract：:The location of target DNA sequences within chromatin may affect the ability of trans-acting factors to bind cis-elements and regulate gene transcription. To examine the effect of chromatin structure on the ability of the estrogen-estrogen receptor complex (E2R) to bind its respective DNA binding element within the ra...

journal_title：Nucleic acids research

authors： Willis SD,Seyfred MA

更新日期：1996-03-15 00:00:00

abstract：:Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational metho...

journal_title：Nucleic acids research

authors： Oparina NJ,Kalinina OV,Gelfand MS,Kisselev LL

更新日期：2005-09-14 00:00:00

abstract：:The intron 2 of the murine thymidine kinase (TK) gene was observed to contain two DNase hypersensitive site. In vitro footprinting experiments indicated specific binding sites for nuclear proteins which were characterized within the sequence of intron 2. Two GC boxes (binding sites for transcription factor SP1) and tw...

journal_title：Nucleic acids research

authors： Rotheneder H,Grabner M,Wintersberger E

更新日期：1991-12-25 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：:KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NI...

journal_title：Nucleic acids research

authors： Chen XW,Jeong JC,Dermyer P

更新日期：2011-01-01 00:00:00

abstract：:Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms, belonging to user-specified phylogenetic clades or taxa. The server takes a set of non-aligned protein cod...

journal_title：Nucleic acids research

authors： Contreras-Moreira B,Sachman-Ruiz B,Figueroa-Palacios I,Vinuesa P

更新日期：2009-07-01 00:00:00