ArticleNucleic acids research2014
The conformational state of the nucleosome entry-exit site modulates TATA box-specific TBP binding.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 21 citations in OpenAlex.
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution.Biophysical journal · 2018Article
- The role of DNA sequence in nucleosome breathing.The European physical journal. E, Soft matter · 2017Article
- Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells.Nature reviews. Genetics · 2017Review
- Quaternary interactions and supercoiling modulate the cooperative DNA binding of AGT.Nucleic acids research · 2017Article
- An Essential Viral Transcription Activator Modulates Chromatin Dynamics.PLoS pathogens · 2016Article
- Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.Biochemical and biophysical research communications · 2016Article
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Structure of silent transcription intervals and noise characteristics of mammalian genes.Molecular systems biology · 2015Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is needed. Using bulk and single-molecule FRET, we find that TBP binds a minimal consensus TATA box as a two-state equilibrium process, showing no evidence for intermediate states. However, upon addition of flanking DNA sequence, we observe non-specific cooperative binding to multiple DNA sites that compete for TATA-box specificity. Thus, we conclude that TBP binding is defined by a branched pathway, wherein TBP initially binds with little sequence specificity and is thermodynamically positioned by its kinetic stability to the TATA box. Furthermore, we observed the real-time access of TBP binding to TATA box DNA located within the DNA entry-exit site of the nucleosome. From these data, we determined salt-dependent changes in the nucleosome conformation regulate TBP's access to the TATA box, where access is highly constrained under physiological conditions, but is alleviated by histone acetylation and TFIIA.
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