ArticleProceedings of the National Academy of Sciences of the United States of America2000
An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 35 citations in OpenAlex.
- DNA superhelicity.Nucleic acids research · 2024Article
- Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling.Nucleic acids research · 2019Article
- DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?Computational and structural biotechnology journal · 2019Review
- Unravelling the Role of the F55 Regulator in the Transition from Lysogeny to UV Induction of Sulfolobus Spindle-Shaped Virus 1.Journal of virology · 2015Article
- Torsion-mediated interaction between adjacent genes.PLoS computational biology · 2014Article
- A new paradigm for transcription factor TFIIB functionality.Scientific reports · 2014Article
- Theoretical analysis of competing conformational transitions in superhelical DNA.PLoS computational biology · 2012Article
- Mechanics of the IL2RA gene activation revealed by modeling and atomic force microscopy.PloS one · 2011Article
- DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation.Nucleic acids research · 2010Article
- A nonlinear dynamic model of DNA with a sequence-dependent stacking term.Nucleic acids research · 2009Article
- Toward a detailed description of the thermally induced dynamics of the core promoter.PLoS computational biology · 2009Article
- Superhelical destabilization in regulatory regions of stress response genes.PLoS computational biology · 2008Article
- Large-scale structural analysis of the core promoter in mammalian and plant genomes.Nucleic acids research · 2005Article
- Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters.Genome research · 2004Article
- From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2003Review
- Targeted histone acetylation at the yeast CUP1 promoter requires the transcriptional activator, the TATA boxes, and the putative histone acetylase encoded by SPT10.Molecular and cellular biology · 2002Article
- Remodeling of yeast CUP1 chromatin involves activator-dependent repositioning of nucleosomes over the entire gene and flanking sequences.Molecular and cellular biology · 2001Article
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Purified RNA polymerase II initiated transcription from the yeast CUP1 promoter fused to a C-less cassette if the DNA was negatively supercoiled. Relaxed plasmid was not transcribed. Transcription did not require addition of any other transcription factors. TATA box-binding protein (TBP) was not detectable in the polymerase preparation and the TATA box was not required. Deletion analysis of the CUP1 promoter revealed that a 25-bp element containing the initiation region was sufficient for recognition by polymerase. Two transcription start sites were mapped, one of which is identical to one of the two major start sites observed in vivo. Our observations can be accounted for by using a theoretical analysis of the probability of DNA melting within the plasmid as a function of superhelix density: the CUP1 initiation element is intrinsically unstable to superhelical stress, permitting entry of the polymerase, which then scans the DNA to locate the start site. In support of this analysis, the CUP1 promoter was sensitive to mung bean nuclease. These observations and a previous theoretical analysis of yeast genes support the idea that promoters are stress points within the DNA superhelix. The role of transcription factors might be to mark the promoter and to regulate specific melting of promoter DNA.
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