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 rat prolactin (rPRL) gene and modulate rPRL gene expression, we have developed cell lines derived from the rPRL-expressing (rPRL+) rat pituitary cell line GH3 and the rPRL-non- expressing (rPRL-) rat embryo fibroblast cell line Rat1. These cell lines contain mini-chromosomes composed of the 5' upstream regulatory region of the rPRL gene driving expression of a reporter gene, Tn5, within a bovine papillomavirus (BPV) vector. The rPRL-Tn5 gene retains the characteristics of cell-specific expression and estrogen inducibility of transcription displayed by the endogenous rPRL gene. The distal enhancer region, which contains an estrogen response element, was found to exist in a nucleosome-free region in pituitary-derived cells even in the absence of estrogen. In contrast, the rPRL distal enhancer in fibroblast cells was found to be randomly packaged into nucleosomes. These results indicate that DNA sequence is not sufficient to position nucleosomes in the rPRL gene. Rather, it suggests that cell-specific factors are present in pituitary cells that modify the chromatin structure of the distal enhancer which allow E2R to bind to its response element.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Willis SD,Seyfred MAdoi
10.1093/nar/24.6.1065subject
Has Abstractpub_date
1996-03-15 00:00:00pages
1065-72issue
6eissn
0305-1048issn
1362-4962pii
5e0725journal_volume
24pub_type
杂志文章abstract：:The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outco...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg096
更新日期：2003-01-01 00:00:00
abstract：:Detailed models are presented for the triple-stranded polynucleotide helices of poly (U)-poly (A)-poly (U) (two forms), poly (U)-poly d (A) -poly (U), poly d(C)-poly d(I)-poly d(C), poly d(T)-polyd(A)-poly d(T) and poly (I)-poly (A)-poly (I). The models were genrated using a computerized, linked-atom procedure which p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.10.2459
更新日期：1976-10-01 00:00:00
abstract：:We have used in vitro transcription in isolated pea nuclei to determine whether the expression of genes for the seed storage proteins legumin and vicilin is regulated transcriptionally or post-transcriptionally in response to changing sulfur status in the developing seed. During the first 48 h of recovery from S defic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.3.999
更新日期：1985-02-11 00:00:00
abstract：:A class II site-specific endodeoxyribonuclease (SalPI) was identified in cell-free extracts of Streptomyces albus CMI 52766 after high speed centrifugation and fractionation through Bio Gel AO.5M. SalPI cleaves lambda DNA into at least 18 fragments. Five cleavage sites were located in the linear lambda map by the use ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.6.1989
更新日期：1977-06-01 00:00:00
abstract：:It is believed that depending on the thermodynamic stability of the 5'-strand and the 3'-strand in the stem-loop structure of a precursor microRNA (pre-miRNA), cells preferentially select the less stable one (called the miRNA or guide strand) and destroy the other one (called the miRNA* or passenger strand). However, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm641
更新日期：2007-01-01 00:00:00
abstract：:The rolling circle DNA replication structures generated by the in vitro phage T4 replication system were analyzed using two-dimensional agarose gels. Replication structures were generated in the presence or absence of T4 primase (gp61), permitting the analysis of replication forks with either duplex or single-stranded...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.11.2166
更新日期：1996-06-01 00:00:00
abstract：:Influenza viruses have a segmented viral RNA (vRNA) genome, which is replicated by the viral RNA-dependent RNA polymerase (RNAP). Replication initiates on the vRNA 3' terminus, producing a complementary RNA (cRNA) intermediate, which serves as a template for the synthesis of new vRNA. RNAP structures show the 3' termi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw884
更新日期：2016-12-01 00:00:00
abstract：:Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.3.629
更新日期：1983-02-11 00:00:00
abstract：:Chromatin fragments released from intact Friend erythroleukemia cell nuclei during limited incubation with micrococcal nuclease, DNase II or DNase I were analyzed to determine the distribution of DNA methyltransferase in chromatin. The enzyme was released in a free form when internucleosomal DNA was digested with micr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5359
更新日期：1981-10-24 00:00:00
abstract：:DNA assembly allows individual DNA constructs or libraries to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable 'scar' sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinato...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1182
更新日期：2019-02-20 00:00:00
abstract：:Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa918
更新日期：2021-01-08 00:00:00
abstract：:Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to dele...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku576
更新日期：2014-09-01 00:00:00
abstract：:EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.56
更新日期：2000-01-01 00:00:00
abstract：:Post-transcriptional gene regulation is mediated through complex networks of protein-RNA interactions. The targets of only a few RNA binding proteins (RBPs) are known, even in the well-characterized budding yeast. In silico prediction of protein-RNA interactions is therefore useful to guide experiments and to provide ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr160
更新日期：2011-08-01 00:00:00
abstract：:In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.14.3433
更新日期：1998-07-15 00:00:00
abstract：:A frequently used method of comparing large RNA molecules employs the two-dimensional display of oligonucleotides generated through the action of specific RNases (oligonucleotide mapping, fingerprinting). Using computer simulations and simple analytic expressions the number of large RNase T1-resistant oligonucleotides...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.1.237
更新日期：1982-01-11 00:00:00
abstract：:DNA replication of phi29 and related phages takes place via a strand displacement mechanism, a process that generates large amounts of single-stranded DNA (ssDNA). Consequently, phage-encoded ssDNA-binding proteins (SSBs) are essential proteins during phage phi29-like DNA replication. In the present work we analyze th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.10.2034
更新日期：2000-05-15 00:00:00
abstract：:The metazoan cell cycle-regulated histone mRNAs are the only known cellular mRNAs that do not terminate in a poly(A) tall. Instead, mammalian histone mRNAs terminate in a highly conserved stem-loop structure which is required for 3'-end processing and regulates mRNA stability. The poly(A) tail not only regulates trans...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.10.1954
更新日期：1996-05-15 00:00:00
abstract：:RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz427
更新日期：2019-06-20 00:00:00
abstract：:cDNA expression libraries displayed on lambda phage have been successfully employed to identify partners involved in antibody-antigen, protein- protein and DNA-protein interactions and represent a novel approach to functional genomics. However, as in all other cDNA expression libraries based on fusion to a carrier pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf077
更新日期：2002-08-01 00:00:00
abstract：:An open reading frame upstream from nifHDK operon of Klebsiella pneumoniae had been described. The orientation of this open reading frame is opposite to that of nifHDK and sequence homology was found between the open reading frame promoter and the promoter of nifHDK operon. A recombinant plasmid carrying the promoter ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.12.4241
更新日期：1983-06-25 00:00:00
abstract：:Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2, which functions in mRNA biogenesis and export. Here, we investigate th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt272
更新日期：2013-06-01 00:00:00
abstract：:Scanning tunneling microscopy (STM) reveals nanometer scale details of hydrated DNA but the interpretation of the images is controversial because of substrate artifacts and the lack of a theory for image contrast. We demonstrate that we have overcome these problems by identifying five DNA samples by their STM images a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.25.5896
更新日期：1993-12-25 00:00:00
abstract：:Scanning force microscopy was used to examine DNA condensates prepared with varying stoichiometries of lipospermine or polyethylenimine in physiological solution. For the first time, individual DNA strands were clearly visualized in incomplete condensates without drying. Using lipospermine at sub-saturating concentrat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.15.3095
更新日期：1997-08-01 00:00:00
abstract：:Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz553
更新日期：2019-09-05 00:00:00
abstract：:The Metabolic Pathway Collection from EMP is an extraction of data from the larger Enzymes and Metabolic Pathways database (EMP). This extraction has been made publicly available in the hope that others will find it useful for a variety of purposes. The original release in October 1995 contained 1814 distinct pathways...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.1.37
更新日期：1997-01-01 00:00:00
abstract：:By screening a rabbit reticulocyte library, an alternative 15-LOX transcript of 3.6 kb (15-LOX mRNA2) was detected containing a 1019 nt longer 3'-untranslated region (UTR2) than the main 2.6 kb mRNA (15-LOX mRNA1). In anaemic animals, northern blotting showed that 15-LOX mRNA2 was predominantly expressed in non-erythr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.8.1828
更新日期：1999-04-15 00:00:00
abstract：:The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting this important resource to the scientific community to support and accelerate the global research effort. Here, we o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1078
更新日期：2019-01-08 00:00:00
abstract：:The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila virilis was investigated by Me3 psoralen photoreaction of mitochondria isolated from embryos. After photoreaction the mtDNA was purified and the pattern of DNA cross-linking was determined by electron microscopy of the DNA under totally denaturing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.4.1991
更新日期：1984-02-24 00:00:00
abstract：:Peptides of defined length carrying a diazirine photoaffinity label attached either to the alpha-NH2 group of the N-terminal methionine residue, or to the epsilon-NH2 group of an immediately adjacent lysine residue, were prepared in situ on Escherichia coli ribosomes in the presence of a synthetic mRNA analogue. Pepti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.8.1394
更新日期：1994-04-25 00:00:00
