Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Hieb, Aaron R., Gansen, Alexander, Böhm, Vera, Langowski, Jörg
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
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
_version_ 1782324057482461184
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
work_keys_str_mv AT hiebaaronr theconformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding
AT gansenalexander theconformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding
AT bohmvera theconformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding
AT langowskijorg theconformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding
AT hiebaaronr conformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding
AT gansenalexander conformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding
AT bohmvera conformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding
AT langowskijorg conformationalstateofthenucleosomeentryexitsitemodulatestataboxspecifictbpbinding