Abstract：
:The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mapping experiments for individual genes, or, starting from release 73, from mass genome annotation projects. Subsets of promoter sequences with customized 5' and 3' extensions can be downloaded from the EPD website. The focus of current development efforts is to reach complete promoter coverage for important model organisms as soon as possible. To speed up this process, a new class of preliminary promoter entries has been introduced as of release 83, which requires less stringent admission criteria. As part of a continuous integration process, new web-based interfaces have been developed, which allow joint analysis of promoter sequences with other bioinformatics resources developed by our group, in particular programs offered by the Signal Search Analysis Server, and gene expression data stored in the CleanEx database. EPD can be accessed at http://www.epd.isb-sib.ch.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schmid CD,Perier R,Praz V,Bucher Pdoi
10.1093/nar/gkj146keywords:
subject
Has Abstractpub_date
2006-01-01 00:00:00pages
D82-5issue
Database issueeissn
0305-1048issn
1362-4962pii
34/suppl_1/D82journal_volume
34pub_type
历史文章,杂志文章abstract：:The VS ribozyme trans-cleavage substrate interacts with the catalytic RNA via tertiary interactions. To study the role of phosphate groups in the ribozyme-substrate interaction, 18 modified substrates were synthesized, where an epimeric phosphorothioate replaces one of the phosphate diester linkages. Sites in the stem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh957
更新日期：2004-12-01 00:00:00
abstract：:Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx616
更新日期：2017-09-19 00:00:00
abstract：:Phospho3D is a database of three-dimensional (3D) structures of phosphorylation sites (P-sites) derived from the Phospho.ELM database, which also collects information on the residues surrounding the P-site in space (3D zones). The database also provides the results of a large-scale structural comparison of the 3D zone...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq936
更新日期：2011-01-01 00:00:00
abstract：:7SK snRNA, an abundant RNA discovered in human nucleus, regulates transcription by RNA polymerase II (RNAPII). It sequesters and inhibits the transcription elongation factor P-TEFb which, by phosphorylation of RNAPII, switches transcription from initiation to processive elongation and relieves pauses of transcription....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq660
更新日期：2010-11-01 00:00:00
abstract：:Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku269
更新日期：2014-06-01 00:00:00
abstract：:The base pairing properties of oligonucleotide duplexes containing 8-aza-7-deaza-2'-deoxyisoguanosine, its 7-bromo or its 7-iodo derivative are described. The nucleosides were synthesized on a convergent route, protected and converted into phosphoramidites. Oligonucleotides were prepared on a solid-phase and were hybr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg926
更新日期：2003-12-15 00:00:00
abstract：:Eukaryotic cellular mRNAs contain a cap at their 5'-ends, but some viral and cellular mRNAs bypass the cap-dependent mechanism of translation initiation in favor of internal entry of ribosomes at specific RNA sequences. Cap-dependent initiation requires intact initiation factor eIF4G (formerly eIF-4gamma, eIF-4Fgamma ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.2.395
更新日期：1997-01-15 00:00:00
abstract：:Gene expression circuitries, which enable cells to detect precise levels within a morphogen concentration gradient, have a pivotal impact on biological processes such as embryonic pattern formation, paracrine and autocrine signalling, and cellular migration. We present the rational synthesis of a synthetic genetic cir...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq671
更新日期：2010-10-01 00:00:00
abstract：:USF is a helix-loop-helix transcription factor that, like Myc, recognizes the DNA binding motif CACGTG. Two different forms of USF, characterized by apparent molecular weights of 43,000 and 44,000, were originally identified in HeLa cells by biochemical analysis. Clones for the 43-kDa USF were first characterized, but...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.3.427
更新日期：1994-02-11 00:00:00
abstract：:The prime mechanism by which p53 acts as a tumor suppressor is as a transcription factor regulating the expression of diverse downstream genes. The DNA-binding domain of p53 (p53DBD) interacts with defined DNA sites and is the main target for mutations in human primary tumors. Here, we show that the CWWG motif, found ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1044
更新日期：2011-03-01 00:00:00
abstract：:The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To understand p53's essential transcriptional functions, unbiased analysis of its DNA-binding repertoire is pivotal. In a genome-wide tiling ChIP-on-chip approach...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn232
更新日期：2008-06-01 00:00:00
abstract：:Identification of components essential to chromosome structure and behaviour remains a vibrant area of study. We have previously shown that invadolysin is essential in Drosophila, with roles in cell division and cell migration. Mitotic chromosomes are hypercondensed in length, but display an aberrant fuzzy appearance....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv211
更新日期：2015-04-20 00:00:00
abstract：:Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genom...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr017
更新日期：2011-05-01 00:00:00
abstract：:The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.20.3910
更新日期：2000-10-15 00:00:00
abstract：:The synthesis of oligonucleotides (ODNs) containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine (D) is described, and thermal stability and resistance to enzymatic hydrolysis of the ODNs are compared with ODNs containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine (H). The ODNs containing D and the complementary RNA de...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg374
更新日期：2003-05-15 00:00:00
abstract：:Genetic screens in Saccharomyces cerevisiae have identified the roles of ribosome components, tRNAs and translation factors in translational fidelity. These screens rely on the suppression of altered start codons, nonsense codons or frameshift mutations in genes involved in amino acid or nucleotide metabolism. Many of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki765
更新日期：2005-08-12 00:00:00
abstract：:We have exploited properties of photosensitizers to study an aspect of the packing of chromatin in the cell nucleus. The fluorescent photosensitizers mesotetra(3-hydroxyphenyl) porphyrin and Photofrin II were both localized in the nuclear membrane and other membrane structures, but could not be found inside the nuclei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.24.6687
更新日期：1992-12-25 00:00:00
abstract：:The 5' processing of rat pre-tRNA(Lys) and a series of mutant derivatives by rat cytosolic RNase P was examined. In standard, non-kinetic assays, mutant precursors synthesized in vitro with 5' leader sequences of 10, 17, 24, 25, and 46 nucleotides were processed to approximately equal levels and yielded precisely clea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.16.3347
更新日期：1994-08-25 00:00:00
abstract：:The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz898
更新日期：2020-01-08 00:00:00
abstract：:The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkaa261
更新日期：2020-05-21 00:00:00
abstract：:BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We dete...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky784
更新日期：2018-11-02 00:00:00
abstract：:TFIIH is a multisubunit factor essential for transcription initiation and promoter escape of RNA polymerase II and for the opening of damaged DNA double strands in nucleotide excision repair (NER). In this study, we have analyzed at which step of the transcription cycle TFIIH is essential for transcription by RNA poly...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr746
更新日期：2012-01-01 00:00:00
abstract：:The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal ade...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki209
更新日期：2005-01-26 00:00:00
abstract：:Herpes simplex type 1 virus (HSV-1) and bacteriophage λ capsids undergo considerable structural changes during self-assembly and DNA packaging. The initial steps of viral capsid self-assembly require weak, non-covalent interactions between the capsid subunits to ensure free energy minimization and error-free assembly....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku634
更新日期：2014-08-01 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
pub_type： 杂志文章
doi：10.1093/nar/15.22.9163
更新日期：1987-11-25 00:00:00
abstract：:Calf thymus DNA polymerase alpha (pol alpha) and bacteriophage T4 DNA polymerase (pol T4) were exploited as model enzymes to investigate the molecular mechanism of inhibitory action of N2-(p-n-butylphenyl)dGTP (BuPdGTP) and 2-(p-n-butyl-anilino)dATP (BuAdATP) on the BuPdNTP-susceptible alpha polymerase family. Kinetic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.7.1627
更新日期：1991-04-11 00:00:00
abstract：:Discovering which regulatory proteins, especially transcription factors (TFs), are active under certain experimental conditions and identifying the corresponding binding motifs is essential for understanding the regulatory circuits that control cellular programs. The experimental methods used for this purpose are labo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp554
更新日期：2009-09-01 00:00:00
abstract：:Mature chicken erythrocyte polynucleosomes which are soluble at physiological ionic strength are enriched in beta-globin DNA sequences. Vitellogenin chromatin, which is not expressed in this tissue, is found in aggregation prone, salt insoluble chromatin. There is a direct correlation between the size of soluble fragm...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.3.1081
更新日期：1987-02-11 00:00:00
abstract：:The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called 'K*Sync', in which alignments are generated by dynamic program...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl480
更新日期：2006-01-01 00:00:00
abstract：:Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contami...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky948
更新日期：2019-01-08 00:00:00
