Abstract:
:We show that in mouse myoblasts the MyoD1 promoter is highly stimulated by MyoD1 expression, suggesting that it is controlled by a positive feedback loop. Using deletion and mutation analyses, we identified the targets for MyoD1 promoter autoregulation as the two proximal E-boxes located close to the MyoD1 core promoter. Gel mobility shift competition assays with MyoD1 antibodies as competitor suggest that the MyoD1 protein is binding directly to these E-boxes. Autoregulation did not occur in fibroblasts cotransfected with the expression vector of MyoD1. It is assumed that autoregulation is controlled by the stoichiometry between the MyoD1 protein and negatively regulatory proteins like Id, which is known to be highly expressed in fibroblasts. When the MyoD1 promoter was methylated, autoregulation only occurred when the density of methylated sites was low. The density of DNA methylation, therefore, can determine the accessibility of the MyoD1 promoter to transcription factors and interfere with the auto- and crossregulatory loop. The MyoD1 promoter in vivo was found to be only partially methylated in all tissues tested except in skeletal muscle where it was demethylated. We propose that high level expression of the MyoD1 gene is a result of release from constraints such as negative regulatory factors and/or DNA methylation interfering with MyoD1 autoregulation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zingg JM,Pedraza-Alva G,Jost JPdoi
10.1093/nar/22.12.2234subject
Has Abstractpub_date
1994-06-25 00:00:00pages
2234-41issue
12eissn
0305-1048issn
1362-4962journal_volume
22pub_type
杂志文章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::Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.14.5545
更新日期:1987-07-24 00:00:00
abstract::A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.14.5651
更新日期:1986-07-25 00:00:00
abstract::Transcription of tRNA-encoding genes by RNA polymerase (Pol) III requires the six-subunit general transcription factor IIIC that uses subcomplexes τA and τB to recognize two gene-internal promoter elements named A- and B-box. The Schizosaccharomyces pombe τA subcomplex comprises subunits Sfc1, Sfc4 and Sfc7. The cryst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt664
更新日期:2013-10-01 00:00:00
abstract::Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1067
更新日期:2009-04-01 00:00:00
abstract::According to the recruitment model of transcriptional activation, an activator helps initiate transcription by bringing the RNA polymerase to a specific location on the DNA through interaction with components of the transcriptional machinery. However, it is difficult to isolate and define the activities of specific ac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1227
更新日期:2010-04-01 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
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky549
更新日期:2018-09-06 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa896
更新日期:2020-11-18 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.11.2006
更新日期:1995-06-11 00:00:00
abstract::The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq318
更新日期:2010-07-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1223
更新日期:2016-03-18 00:00:00
abstract::LINE-1 (L1) is a highly successful autonomous non-LTR retrotransposon and a major force shaping mammalian genomes. Although there are about 600 000 L1 copies covering 23% of the rat genome, full-length rat L1s (L1Rn) with intact open reading frames (ORFs) representing functional master copies for retrotransposition ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1045
更新日期:2008-02-01 00:00:00
abstract::PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1040
更新日期:2015-01-01 00:00:00
abstract::One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of regulatory motifs playing key roles in the regulation of gene expression at transcriptional and post-tran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh465
更新日期:2004-07-01 00:00:00
abstract::Overexpressed in colon carcinoma-1 (OCC-1) is one of the earliest annotated long noncoding RNAs (lncRNAs) in colorectal cancer (CRC); however, its function remains largely unknown. Here, we revealed that OCC-1 plays a tumor suppressive role in CRC. OCC-1 knockdown by RNA interference promotes cell growth both in vitro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky214
更新日期:2018-06-20 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.1.154
更新日期:1995-01-11 00:00:00
abstract::Predicting molecular interactions is a major goal in rational drug design. Pharmacophore, which is the spatial arrangement of features that is essential for a molecule to interact with a specific target receptor, is an important model for achieving this goal. We present a freely available web server, named PharmaGist,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn187
更新日期:2008-07-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv760
更新日期:2015-09-18 00:00:00
abstract::Eukaryotes produce multiple products from a single gene locus by alternative splicing, translation or promoter usage as mechanisms expanding the complexity of their proteome. Trithorax proteins, including the Arabidopsis Trithorax-like protein ATX1, are histone modifiers regulating gene activity. Here, we report that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1300
更新日期:2011-06-01 00:00:00
abstract::We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3722
更新日期:1996-10-01 00:00:00
abstract::Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp490
更新日期:2009-08-01 00:00:00
abstract::In some preparations of DNA dependent RNA polymerase a new enzymatic activity has been found which catalyzes the condensation of two pyrophosphate molecules, liberated in the process of RNA synthesis, to one molecule of orthophosphate and one molecule of Mg (or Mn) - chelate complex with trimetaphosphate. This activit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.4.1521
更新日期:1979-04-01 00:00:00
abstract::Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2723
更新日期:1998-06-01 00:00:00
abstract::Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr987
更新日期:2012-01-01 00:00:00
abstract::Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesion...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky386
更新日期:2018-06-20 00:00:00
abstract::Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1319
更新日期:2019-04-08 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh734
更新日期:2004-07-27 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky835
更新日期:2018-11-16 00:00:00
abstract::Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky084
更新日期:2018-04-06 00:00:00