Pituitary-specific chromatin structure of the rat prolactin distal enhancer element.


: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.


Nucleic Acids Res


Nucleic acids research


Willis SD,Seyfred MA




Has Abstract


1996-03-15 00:00:00














  • All three functional domains of the large ribosomal subunit protein L25 are required for both early and late pre-rRNA processing steps in Saccharomyces cerevisiae.

    abstract::Mutational analysis has shown that the integrity of the region in domain III of 25S rRNA that is involved in binding of ribosomal protein L25 is essential for the production of mature 25S rRNA in the yeast Saccharomyces cerevisiae. However, even structural alterations that do not noticeably affect recognition by L25, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: van Beekvelt CA,de Graaff-Vincent M,Faber AW,van't Riet J,Venema J,Raué HA

    更新日期:2001-12-15 00:00:00

  • Recognition of distinct HLA-DQA1 promoter elements by a single nuclear factor containing Jun and Fos or antigenically related proteins.

    abstract::The activity of MHC class II promoters depends upon conserved regulatory signals one of which, the extended X-box, contains in its X2 subregion a sequence related to the cAMP response element, CRE and to the TPA response element, TRE. Accordingly, X2 is recognized by the AP-1 factor and by other c-Jun or c-Fos contain...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Neve Ombra M,Autiero M,DeLerma Barbaro A,Barretta R,Del Pozzo G,Guardiola J

    更新日期:1993-04-25 00:00:00

  • Elk-1 can recruit SRF to form a ternary complex upon the serum response element.

    abstract::The initial genomic response to serum growth factors is the transcriptional activation of a set of immediate-early genes. Serum-induced transcriptional activation of several of these genes involves the formation of a ternary complex that includes the serum response factor (SRF), a 62 kDa ternary complex factor (TCF) a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Latinkić BV,Zeremski M,Lau LF

    更新日期:1996-04-01 00:00:00

  • SMAR1 and Cux/CDP modulate chromatin and act as negative regulators of the TCRbeta enhancer (Ebeta).

    abstract::Chromatin modulation at various cis-acting elements is critical for V(D)J recombination during T and B cell development. MARbeta, a matrix-associated region (MAR) located upstream of the T cell receptor beta (TCRbeta) enhancer (Ebeta), serves a crucial role in silencing Ebeta-mediated TCR activation. By DNaseI hyperse...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kaul-Ghanekar R,Jalota A,Pavithra L,Tucker P,Chattopadhyay S

    更新日期:2004-09-15 00:00:00

  • Nuclear dynamics of topoisomerase IIβ reflects its catalytic activity that is regulated by binding of RNA to the C-terminal domain.

    abstract::DNA topoisomerase II (topo II) changes DNA topology by cleavage/re-ligation cycle(s) and thus contributes to various nuclear DNA transactions. It is largely unknown how the enzyme is controlled in a nuclear context. Several studies have suggested that its C-terminal domain (CTD), which is dispensable for basal relaxat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Onoda A,Hosoya O,Sano K,Kiyama K,Kimura H,Kawano S,Furuta R,Miyaji M,Tsutsui K,Tsutsui KM

    更新日期:2014-08-01 00:00:00

  • ModBase, a database of annotated comparative protein structure models and associated resources.

    abstract::ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modelle...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pieper U,Webb BM,Dong GQ,Schneidman-Duhovny D,Fan H,Kim SJ,Khuri N,Spill YG,Weinkam P,Hammel M,Tainer JA,Nilges M,Sali A

    更新日期:2014-01-01 00:00:00

  • Comparison of antiparallel A.AT and T.AT triplets within an alternate strand DNA triple helix.

    abstract::We have examined the formation of alternate strand triple-helices at the target sequence A11(TC)6.(GA)6T11 using the oligonucleotides T11(AG)6 and T11(TG)6, by DNase I footprinting. These third strands were designed so as to form parallel T.AT triplets together with antiparallel G.GC and A.AT or T.AT triplets. We find...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Washbrook E,Fox KR

    更新日期:1994-09-25 00:00:00

  • The genome portal of the Department of Energy Joint Genome Institute.

    abstract::The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintai...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grigoriev IV,Nordberg H,Shabalov I,Aerts A,Cantor M,Goodstein D,Kuo A,Minovitsky S,Nikitin R,Ohm RA,Otillar R,Poliakov A,Ratnere I,Riley R,Smirnova T,Rokhsar D,Dubchak I

    更新日期:2012-01-01 00:00:00

  • GenBank.

    abstract::The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Benson DA,Boguski MS,Lipman DJ,Ostell J,Ouellette BF

    更新日期:1998-01-01 00:00:00

  • DNA intercalation without flipping in the specific ThaI-DNA complex.

    abstract::The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Firczuk M,Wojciechowski M,Czapinska H,Bochtler M

    更新日期:2011-01-01 00:00:00

  • The Schizosaccharomyces pombe mgU6-47 gene is required for 2'-O-methylation of U6 snRNA at A41.

    abstract::Through a computer search of DNA databases, we have identified the homologs of the mgU6-47 snoRNA gene from the yeast Schizosaccharomyces pombe, the fly Drosophila melanogaster and human. The three box C/D-containing snoRNA genes showed no significant similarity in their sequences except for an 11 nt long complementar...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhou H,Chen YQ,Du YP,Qu LH

    更新日期:2002-02-15 00:00:00

  • Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies.

    abstract::Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Salari R,Kimchi-Sarfaty C,Gottesman MM,Przytycka TM

    更新日期:2013-01-07 00:00:00

  • Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor.

    abstract::The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and format...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Haiser HJ,Karginov FV,Hannon GJ,Elliot MA

    更新日期:2008-02-01 00:00:00

  • High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

    abstract::In silico prediction of transcription factor binding sites (TFBSs) is central to the task of gene regulatory network elucidation. Genomic DNA sequence information provides a basis for these predictions, due to the sequence specificity of TF-binding events. However, DNA sequence alone is an impoverished source of infor...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Whitington T,Perkins AC,Bailey TL

    更新日期:2009-01-01 00:00:00

  • Smad proteins regulate transcriptional induction of the SM22alpha gene by TGF-beta.

    abstract::Smad proteins transduce signals from transforming growth factor-beta (TGF-beta) receptors and regulate transcription of target genes. TGF-beta is implicated in the regulation of the smooth muscle cell specific gene SM22alpha, but little is known about how Smads are involved in SM22alpha gene transcription. In this rep...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen S,Kulik M,Lechleider RJ

    更新日期:2003-02-15 00:00:00

  • Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.

    abstract::Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (sha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chiu TP,Rao S,Mann RS,Honig B,Rohs R

    更新日期:2017-12-01 00:00:00

  • Some bacterial tRNA genes are transcribed by eukaryotic RNA polymerase III.

    abstract::E. coli genes for tRNAasp and tRNAtrp are transcribed by eukaryotic RNA polymerase III upon injection into nuclei of Xenopus oocytes. This indicates that some bacterial tRNA genes contain RNA polymerase III promoter sequences. We discuss evolutionary aspects of this finding. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Folk WR,Hofstetter H,Birnstiel ML

    更新日期:1982-11-25 00:00:00

  • Improvements to solid phase phosphotriester synthesis of deoxyoligonucleotides.

    abstract::A solution of benzenesulphonic acid (3%, w/v) in a dimethylformamide and dichloromethane mixture (9:1, v/v) is shown to be a very effective reagent for the detritylation of deoxyoligonucleotides attached to a solid support. The levels of depurination with this reagent were lower than those observed with other reagents...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Patel TP,Millican TA,Bose CC,Titmas RC,Mock GA,Eaton MA

    更新日期:1982-09-25 00:00:00

  • Benzpyrene groups bind preferentially to the DNA of active chromatin in human lung cells.

    abstract::The cells of the bronchial epithelium of man are targets for benzo(a)pyrene carcinogenesis. When cultures of these cells, and of non-target fibroblasts, are exposed to [3H]-benzo(a)pyrene, we find that the epithelial cells metabolise and bind to DNA far greater amounts of benzpyrene than do fibroblasts. By analysis of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Arrand JE,Murray AM

    更新日期:1982-03-11 00:00:00

  • Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

    abstract::Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mund C,Beier V,Bewerunge P,Dahms M,Lyko F,Hoheisel JD

    更新日期:2005-04-28 00:00:00

  • Specific binding of o-phenanthroline at a DNA structural lesion.

    abstract::DNA intercalators are found to recognize a DNA lesion as a high affinity receptor site. This lesion-specific binding is observed when one strand of a DNA double helix contains an extra, unpaired nucleotide. Our assay for binding controls for the effects of sequence with a series of oligodeoxynucleotide duplexes which ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Williams LD,Thivierge J,Goldberg IH

    更新日期:1988-12-23 00:00:00

  • RAD51 and mitotic function of mus81 are essential for recovery from low-dose of camptothecin in the absence of the WRN exonuclease.

    abstract::Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Aiello FA,Palma A,Malacaria E,Zheng L,Campbell JL,Shen B,Franchitto A,Pichierri P

    更新日期:2019-07-26 00:00:00

  • A method of one-step enzyme labelling of short oligonucleotide probes for filter hybridisation.

    abstract::Here we describe a method of labelling short oligonucleotide probes with enzyme without purification or chemical modifications. Biotinylated oligonucleotides as short as 10 nt are coupled with streptavidin-conjugated enzyme, hybridised and detected with enzyme-triggered chemiluminescence. The detection of hybridisatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Guerasimova A,Ivanov I,Lehrach H

    更新日期:1999-01-15 00:00:00

  • A yeast transcription system for the 5S rRNA gene.

    abstract::A cell-free extract of yeast nuclei that can specifically transcribe cloned yeast 5S rRNA genes has been developed. Optima for transcription of 5S rDNA were determined and conditions of extract preparation leading to reproducible activities and specificities established. The major in vitro product has the same size an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: van Keulen H,Thomas DY

    更新日期:1982-09-11 00:00:00

  • Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization.

    abstract::The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chan P,Yuen T,Ruf F,Gonzalez-Maeso J,Sealfon SC

    更新日期:2005-10-13 00:00:00

  • Open TG-GATEs: a large-scale toxicogenomics database.

    abstract::Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Igarashi Y,Nakatsu N,Yamashita T,Ono A,Ohno Y,Urushidani T,Yamada H

    更新日期:2015-01-01 00:00:00

  • Having it both ways: transcription factors that bind DNA and RNA.

    abstract::Multifunctional proteins challenge the conventional 'one protein-one function' paradigm. Here we note apparent multifunctional proteins with nucleic acid partners, tabulating eight examples. We then focus on eight additional cases of transcription factors that bind double-stranded DNA with sequence specificity, but th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Cassiday LA,Maher LJ 3rd

    更新日期:2002-10-01 00:00:00

  • Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery.

    abstract::Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Xu P,Modavi C,Demaree B,Twigg F,Liang B,Sun C,Zhang W,Abate AR

    更新日期:2020-05-07 00:00:00

  • Evaluation of phosphodiesterase I-based protocols for the detection of multiply damaged sites in DNA: the detection of abasic, oxidative and alkylative tandem damage in DNA oligonucleotides.

    abstract::It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bowman KJ,Pla RL,Guichard Y,Farmer PB,Jones GD

    更新日期:2001-10-15 00:00:00

  • Molecular structure of (m5 dC-dG)3: the role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA.

    abstract::The hexamer (m5 dC-dG)3 has been synthesized and its three-dimensional structure determined by a single crystal X-ray diffraction analysis. The structure has been refined to a final R value of 15.6% at 1.3 A resolution. The molecule forms a left-handed Z-DNA helix which is similar to the unmethylated Z-DNA structure. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fujii S,Wang AH,van der Marel G,van Boom JH,Rich A

    更新日期:1982-12-11 00:00:00