ArticleNucleic acids research2007
Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
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- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region.BMC plant biology · 2016Article
- The conformational state of the nucleosome entry-exit site modulates TATA box-specific TBP binding.Nucleic acids research · 2014Article
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- 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
- Sequence-dependent cooperative binding of p53 to DNA targets and its relationship to the structural properties of the DNA targets.Nucleic acids research · 2011Article
- Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix.PloS one · 2010Article
- Origins of specificity in protein-DNA recognition.Annual review of biochemistry · 2010Review
- Regulation of CART peptide expression by CREB in the rat nucleus accumbens in vivo.Brain research · 2009Article
- Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.Nucleic acids research · 2008Article
- p53-Induced DNA bending: the interplay between p53-DNA and p53-p53 interactions.The journal of physical chemistry. B · 2008Article
- Functional specificity of a Hox protein mediated by the recognition of minor groove structure.Cell · 2007Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
TBP recognizes its target sites, TATA boxes, by recognizing their sequence-dependent structure and flexibility. Studying this mode of TATA-box recognition, termed 'indirect readout', is important for elucidating the binding mechanism in this system, as well as for developing methods to locate new binding sites in genomic DNA. We determined the binding stability and TBP-induced TATA-box bending for consensus-like TATA boxes. In addition, we calculated the individual information score of all studied sequences. We show that various non-additive effects exist in TATA boxes, dependent on their structural properties. By several criterions, we divide TATA boxes to two main groups. The first group contains sequences with 3-4 consecutive adenines. Sequences in this group have a rigid context-independent cooperative structure, best described by a nearest-neighbor non-additive model. Sequences in the second group have a flexible, context-dependent conformation, which cannot be described by an additive model or by a nearest-neighbor non-additive model. Classifying TATA boxes by these and other structural rules clarifies the different recognition pathways and binding mechanisms used by TBP upon binding to different TATA boxes. We discuss the structural and evolutionary sources of the difficulties in predicting new binding sites by probabilistic weight-matrix methods for proteins in which indirect readout is dominant.
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