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The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding
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 promoter...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081063/ https://www.ncbi.nlm.nih.gov/pubmed/24829456 http://dx.doi.org/10.1093/nar/gku423 |
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author | Hieb, Aaron R. Gansen, Alexander Böhm, Vera Langowski, Jörg |
author_facet | Hieb, Aaron R. Gansen, Alexander Böhm, Vera Langowski, Jörg |
author_sort | Hieb, Aaron R. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4081063 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-40810632014-07-10 The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding Hieb, Aaron R. Gansen, Alexander Böhm, Vera Langowski, Jörg Nucleic Acids Res Gene regulation, Chromatin and Epigenetics 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. Oxford University Press 2014-08-01 2014-05-14 /pmc/articles/PMC4081063/ /pubmed/24829456 http://dx.doi.org/10.1093/nar/gku423 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Gene regulation, Chromatin and Epigenetics Hieb, Aaron R. Gansen, Alexander Böhm, Vera Langowski, Jörg The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding |
title | The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding |
title_full | The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding |
title_fullStr | The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding |
title_full_unstemmed | The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding |
title_short | The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding |
title_sort | conformational state of the nucleosome entry–exit site modulates tata box-specific tbp binding |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081063/ https://www.ncbi.nlm.nih.gov/pubmed/24829456 http://dx.doi.org/10.1093/nar/gku423 |
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