ArticleNucleic acids research2006
TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
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- Unannotated single nucleotide polymorphisms in the TATA box of erythropoiesis genes show in vitro positive involvements in cognitive and mental disorders.BMC medical genetics · 2020Article
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- Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors.Nucleic acids research · 2016Article
- The conformational state of the nucleosome entry-exit site modulates TATA box-specific TBP binding.Nucleic acids research · 2014Article
- Real-Time Interaction between TBP and the TATA Box of the Human Triosephosphate Isomerase Gene Promoter in the Norm and Pathology.Acta naturae · 2014Article
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- Low-level p53 expression changes transactivation rules and reveals superactivating sequences.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Structural features based genome-wide characterization and prediction of nucleosome organization.BMC bioinformatics · 2012Article
- Sequence-dependent cooperative binding of p53 to DNA targets and its relationship to the structural properties of the DNA targets.Nucleic acids research · 2011Article
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- Regulation of CART peptide expression by CREB in the rat nucleus accumbens in vivo.Brain research · 2009Article
- Function and structural organization of Mot1 bound to a natural target promoter.The Journal of biological chemistry · 2008Article
- Formation of an RNA polymerase II preinitiation complex on an RNA promoter derived from the hepatitis delta virus RNA genome.Nucleic acids research · 2008Article
- Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences.The Journal of biological chemistry · 2008Article
- Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box.Nucleic acids research · 2008Article
- Monovalent cation binding by curved DNA molecules containing variable numbers of a-tracts.Biophysical journal · 2008Article
- Generic eukaryotic core promoter prediction using structural features of DNA.Genome research · 2008Article
- Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA.BMC genetics · 2007Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We carried out in vitro selection experiments to systematically probe the effects of TATA-box flanking sequences on its interaction with the TATA-box binding protein (TBP). This study validates our previous hypothesis that the effect of the flanking sequences on TBP/TATA-box interactions is much more significant when the TATA box has a context-dependent DNA structure. Several interesting observations, with implications for protein-DNA interactions in general, came out of this study. (i) Selected sequences are selection-method specific and TATA-box dependent. (ii) The variability in binding stability as a function of the flanking sequences for (T-A)4 boxes is as large as the variability in binding stability as a function of the core TATA box itself. Thus, for (T-A)4 boxes the flanking sequences completely dominate and determine the binding interaction. (iii) Binding stabilities of all but one of the individual selected sequences of the (T-A)4 form is significantly higher than that of their mononucleotide-based consensus sequence. (iv) Even though the (T-A)4 sequence is symmetric the flanking sequence pattern is asymmetric. We propose that the plasticity of (T-A)n sequences increases the number of conformationally distinct TATA boxes without the need to extent the TBP contact region beyond the eight-base-pair long TATA box.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.