Abstract:
:The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. All of the data are accessible via searching by gene or protein name, and are available on the Web at http://www.yeastrc.org/pdr/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Riffle M,Malmström L,Davis TNdoi
10.1093/nar/gki073keywords:
subject
Has Abstractpub_date
2005-01-01 00:00:00pages
D378-82issue
Database issueeissn
0305-1048issn
1362-4962pii
33/suppl_1/D378journal_volume
33pub_type
杂志文章abstract::Recently published alignments of available 5 S rRNA sequences have shown that a rigid base pairing pattern, pointing to the existence of a universal five-helix secondary structure for all 5 S RNAs, can be superimposed on such alignments. For a few species, the alignment and the base pairing pattern show distortions wi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.5.1245
更新日期:1983-03-11 00:00:00
abstract::High-throughput screening assays have been developed to rapidly identify small molecule inhibitors targeting catalytic group I introns. Biochemical reactions catalyzed by a self-splicing group I intron derived from Pneumocystis carinii or from bacteriophage T4 have been investigated. In vitro biochemical assays amenab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.24.5051
更新日期:1996-12-15 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
pub_type: 杂志文章
doi:10.1093/nar/gkz293
更新日期:2019-07-09 00:00:00
abstract::We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1322
更新日期:2017-03-17 00:00:00
abstract::The Bcl-2 protein has an anti-apoptotic effect in neuronal and other cell types. We show for the first time that the Bcl-2 promoter is activated by the neuronal survival factor nerve growth factor (NGF) and that this effect is dependent on a region of the promoter from -1472 to -1414. This activation requires the Rap-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.10.2086
更新日期:1999-05-15 00:00:00
abstract::The agents daunomycin, ethidium bromide, distamycin A and cytochrome c inhibit DNA dependent DNA polymerase I (E. coli) reaction competitively to DNA. The influence of these template inactivators on the binding of DNA polymerase to native as well as denatured DNA has been determined by affinity chromatography. Cytochr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.1.63
更新日期:1974-01-01 00:00:00
abstract::The sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA has been determined. The sequence contains the entire coat protein cistron as well as regions to its left and right. Sequence characterization was by conventional methods for use with uniformly 32P labeled RNA complemented by newer methods for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.4.1287
更新日期:1979-04-01 00:00:00
abstract::Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt423
更新日期:2013-08-01 00:00:00
abstract::The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr214
更新日期:2011-07-01 00:00:00
abstract::Histone variants play an important role in shaping the mammalian epigenome and their aberrant expression is frequently observed in several types of cancer. However, the mechanisms that mediate their function and the composition of the variant-containing chromatin are still largely unknown. A proteomic interrogation of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku303
更新日期:2014-06-01 00:00:00
abstract::A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min. on the bacterial chromosome. The rate of RNA synthesis in vivo and the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.12.3445
更新日期:1990-06-25 00:00:00
abstract::The ribosomal proteins L4 and L22 form part of the peptide exit tunnel in the large ribosomal subunit. In Escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. The structures of the 30S as well as the 50S subunits from each antibiotic resistant mutan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh913
更新日期:2004-10-27 00:00:00
abstract::Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt153
更新日期:2013-04-01 00:00:00
abstract::NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1159
更新日期:2017-01-25 00:00:00
abstract::UMSBP is a CCHC-type zinc finger protein, which functions during replication initiation of kinetoplast DNA minicircles and the segregation of kinetoplast DNA networks. Interactions of UMSBP with origin sequences, as well as the protein oligomerization, are affected by its redox state. Reduction yields UMSBP monomers a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn927
更新日期:2009-01-01 00:00:00
abstract::Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translato...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1034
更新日期:2018-01-04 00:00:00
abstract::The pyrrole-imidazole (Py-Im) triamide-cyclopropa pyrroloindole (CPI) conjugates ImPyImLDu86 (7) and ImImPyLDu86 (14) were synthesized and their alkylating activities and inhibitory effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis demonstrated that conjugates 7 and 14 speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf486
更新日期:2002-09-01 00:00:00
abstract::Argonaute (AGO) proteins have a well-established role in post-transcriptional regulation of gene expression as key component of the RNA silencing pathways. Recent evidence involves AGO proteins in mammalian nuclear processes such as transcription and splicing, though the mechanistic aspects of AGO nuclear functions re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1387
更新日期:2015-02-18 00:00:00
abstract::The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki317
更新日期:2005-03-23 00:00:00
abstract::Minimized trans-acting HDV ribozyme systems consisting of three (Rz-3) and two (Rz-2) RNA strands were prepared and their folding conformations were analyzed by NMR spectroscopy. The guanosine residues in one of the enzyme components of Rz-3 were labeled with 13C and 15N. Imino proton signals were assigned by analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.3.766
更新日期:2002-02-01 00:00:00
abstract::The evolution of regulatory networks in Bacteria has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations fas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa162
更新日期:2020-05-07 00:00:00
abstract::Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essentia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1165
更新日期:2017-01-25 00:00:00
abstract::We took advantage of the unusual genomic organization of the ciliate Oxytricha trifallax to screen for eukaryotic non-coding RNA (ncRNA) genes. Ciliates have two types of nuclei: a germ line micronucleus that is usually transcriptionally inactive, and a somatic macronucleus that contains a reduced, fragmented and rear...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr501
更新日期:2011-09-01 00:00:00
abstract::Chromatin footprinting in Drosophila tissue culture cells has detected the binding of a non-histone protein at +8 of the distal Adh RNA start site, on a 10-bp direct repeat motif abutting a nucleosome positioned over the inactive Adh distal promoter. Alternatively the active promoter is bound by a transcription initia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.17.4481
更新日期:1992-09-11 00:00:00
abstract::Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage 29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks724
更新日期:2012-10-01 00:00:00
abstract::DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pat...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gku284
更新日期:2014-06-01 00:00:00
abstract::In many eukaryotic mRNAs one or more short 'upstream' open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkp1037
更新日期:2010-01-01 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
pub_type: 杂志文章
doi:10.1093/nar/gku978
更新日期:2014-12-01 00:00:00
abstract::Mitochondrial transcription factor A (TFAM) stimulates transcription from mitochondrial DNA (mtDNA) promoters in vitro and in organello. To investigate whether changes of TFAM levels also modulate transcription and replication in situ, the protein was transiently overexpressed in cultured cells. Mitochondrial mRNAs we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh921
更新日期:2004-11-16 00:00:00
abstract::Different pre-ribosomal complexes are formed during ribosome biogenesis, and the composition of these complexes is highly dynamic. Dbp4, a conserved DEAD-box RNA helicase implicated in ribosome biogenesis, interacts with nucleolar proteins Bfr2 and Enp2. We show that, like Dbp4, Bfr2 and Enp2 are required for the earl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1293
更新日期:2014-03-01 00:00:00