Abstract:
:To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferential activation of the proximal promoter in a tandem promoter arrangement has been found before in several laboratories, including our own, but for technical reasons the data were inconclusive with regards to the enhancer mechanism. In the work presented here, we readdress the question of preferential promoter activation by an enhancer using a more clearly defined system. Two identical promoters were kept closeby in a divergent, or directly repeated orientation. The SV40 enhancer was placed at a great distance on one or the other side of the two promoters, to see whether the enhancer position influenced the relative efficiency of the two promoters in transfected cells. Our finding that the promoter usage is virtually unaffected by the enhancer position does not favor a scanning model, but is compatible with a looping model of enhancer action.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Heuchel R,Matthias P,Schaffner Wdoi
10.1093/nar/17.22.8931subject
Has Abstractpub_date
1989-11-25 00:00:00pages
8931-47issue
22eissn
0305-1048issn
1362-4962journal_volume
17pub_type
杂志文章abstract::By in vivo DMS footprint and reporter gene analyses we identified two transcription factor binding sites in the human c-sis/PDGF B gene promoter. The low basal activity of the PDGF B promoter in HeLa and undifferentiated K562 cells, which express low PDGF B mRNA levels, and in PC3 cells, which express a high PDGF B mR...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.7.1119
更新日期:1995-04-11 00:00:00
abstract::Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA damage. Importantly...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr697
更新日期:2012-01-01 00:00:00
abstract::Lambda exonuclease processively degrades one strand of double-stranded DNA (dsDNA) in the 5"-3" direction. To understand the mechanism through which this enzyme generates high processivity we are analyzing the first step in the reaction, namely the interaction of lambda exonuclease with the ends of substrate DNA. Endo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.15.3057
更新日期:1999-08-01 00:00:00
abstract::The nucleotide sequence of the chick beta-actin gene was determined. The gene contains 5 introns; 4 interrupt the translated region at codons 41/42, 120/122, 267, 327/328 and a large intron occurs in the 5' untranslated region. The gene has a 97 nucleotide 5'-untranslated region and a 594 nucleotide 3'-untranslated re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.23.8287
更新日期:1983-12-10 00:00:00
abstract::Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky787
更新日期:2018-10-12 00:00:00
abstract::RNase J is a conserved ribonuclease that belongs to the β-CASP family of nucleases. It possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rRNA maturation and mRNA decay. Here we report high-resolution crystal structures of Deinococcus radiodurans RNase J complexed with RNA or uridine 5'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv444
更新日期:2015-06-23 00:00:00
abstract::DNA restriction fragments located 5' to the human c-myc gene display anomalous electrophoretic mobility on polyacrylamide gels. Computer modeling of the c-myc flanking DNA suggests that the slow-moving DNA fragments spanning nucleotides -1690 to -1054 (relative to c-myc promoter P1) and -718 to -452 form large left ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.7.2819
更新日期:1989-04-11 00:00:00
abstract::The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the F.graminearum genome sequence. A complete manually revised g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj026
更新日期:2006-01-01 00:00:00
abstract::Linkage analysis is a successful procedure to associate diseases with specific genomic regions. These regions are often large, containing hundreds of genes, which make experimental methods employed to identify the disease gene arduous and expensive. We present two methods to prioritize candidates for further experimen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl707
更新日期:2006-01-01 00:00:00
abstract::An updated list of DNA sequences cloned from the human genome over the past year (1991) is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic probes comprising both gene and pseudogene sequences. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.suppl.2181
更新日期:1992-05-11 00:00:00
abstract::In this study we describe a novel method to investigate the RNA-RNA interactions between a small RNA and its target that we termed 'RNA walk'. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT-PCR or real-time...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp872
更新日期:2010-01-01 00:00:00
abstract::Near-UV difference spectral analysis of the triplex formed from d(C-T)6 and d(A-G)6.d(C-T)6 in neutral and acidic solution shows that the third strand dC residues are protonated at pH 7.0, far above their intrinsic pKa. Additional support for ion-dipole interactions between the third strand dC residues and the G.C tar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.14.2692
更新日期:1995-07-25 00:00:00
abstract::The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1012
更新日期:2014-01-01 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::MeCP2 is a methyl-CpG binding protein that can repress transcription of nearby genes. In humans, mutations in the MECP2 gene are the major cause of Rett syndrome. By searching expressed sequence tag (EST) databases we have found a novel MeCP2 splice isoform (MeCP2alpha) which encodes a distinct N-terminus. We demonstr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh349
更新日期:2004-03-19 00:00:00
abstract::The tissue specificity of mitochondrial tRNA mutations remains largely elusive. In this study, we demonstrated the deleterious effects of tRNAThr 15927G>A mutation that contributed to pathogenesis of coronary artery disease. The m.15927G>A mutation abolished the highly conserved base-pairing (28C-42G) of anticodon ste...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1241
更新日期:2019-02-28 00:00:00
abstract::The conformational changes induced by the binding of cis-diamminedichloroplatinum(II) to poly(dG-dC).poly(dG-dC) have been studied by reaction with specific antibodies, by circular dichroism and 31P nuclear magnetic resonance. Polyclonal and monoclonal antibodies to Z-DNA bind to platinated poly(dG-dC).poly(dG-dC) at ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.14.5767
更新日期:1984-07-25 00:00:00
abstract::Diastereomeric dithymidine methanephosphonamidates (TnpmT) were synthesized by reaction of 3'-amino-3'-deoxythymidine with 3'- O -acetylthymidin-5-yl-methanephosphonochloridate. Separated dinucleotide TnpmT(fast) and TnpmT(slow) diastereomers were used as building blocks to prepare chimeric dodecathy-midylates, posses...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2650
更新日期:1998-06-01 00:00:00
abstract::The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1070
更新日期:2013-12-01 00:00:00
abstract::The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu-like RNAs of different evolutionary ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.2.318
更新日期:1997-01-15 00:00:00
abstract::TAP/hNXF1 is a key factor that mediates general cellular mRNA export from the nucleus, and its orthologs are structurally and functionally conserved from yeast to humans. Metazoans encode additional proteins that share homology and domain organization with TAP/hNXF1, suggesting their participation in mRNA metabolism; ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki706
更新日期:2005-07-13 00:00:00
abstract::Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potenti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa889
更新日期:2021-01-08 00:00:00
abstract::Topoisomerase II, purified from chicken erythrocytes, was reacted with a large number of different DNA fragments and cleavages were catalogued in the presence and absence of drugs that stabilize the cleavage intermediate. Cleavages were sequenced to derive a consensus for topoisomerase II that predicts catalytic sites...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5533
更新日期:1988-06-24 00:00:00
abstract::The products of the RAG-1 and RAG-2 genes are essential for the recombination of the DNA encoding the antigen receptors of the developing immune system. Little is known of the specific role these genes play. We have explored the sequences encoding mouse RAG-1 by deleting large parts of the gene and by introducing loca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5644
更新日期:1993-12-11 00:00:00
abstract::During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt728
更新日期:2013-11-01 00:00:00
abstract::The HpaR-mediated regulation of the hpa-meta operon (Pg promoter) of the 4-hydroxyphenylacetic acid catabolic pathway of Escherichia coli has been studied. The HpaR regulator was purified to homogeneity showing that it is able to bind selectively to 4-hydroxyphenylacetic, 3-hydroxyphenylacetic and 3,4-dihydroxyphenyla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg851
更新日期:2003-11-15 00:00:00
abstract::The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families. Each structural family is expanded with domain sequence relatives recruited from GenBank using a variety of efficient seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg062
更新日期:2003-01-01 00:00:00
abstract::Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.4.889
更新日期:1992-02-25 00:00:00
abstract::The double helix is known to form as a result of hybridization of complementary nucleic acid strands in aqueous solution. In the helix the negatively charged phosphate groups of each nucleic acid strand are distributed helically on the outside of the duplex and are available for interaction with cationic groups. Catio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.14.3051
更新日期:2001-07-15 00:00:00
abstract::Oligonucleotides synthesized in array format suffer from contamination by truncated species. We have developed a method to invert DNA molecules in situ after completed synthesis. Reactive functions at the 5'-ends of the oligonucleotides are permitted to react with functions on the support before the 3'-ends are releas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.24.4710
更新日期:1999-12-15 00:00:00