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Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity

Previous studies have analyzed patterns of transcription, transcription factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown. For example, physiologic TF binding s...

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Autores principales: Yadav, Vinod Kumar, Thakur, Ram Krishna, Eckloff, Bruce, Baral, Aradhita, Singh, Ankita, Halder, Rashi, Kumar, Akinchan, Alam, Mohammad Parwez, Kundu, Tapas K., Pandita, Raj, Pandita, Tej K., Wieben, Eric D., Chowdhury, Shantanu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150765/
https://www.ncbi.nlm.nih.gov/pubmed/25081206
http://dx.doi.org/10.1093/nar/gku596
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author Yadav, Vinod Kumar
Thakur, Ram Krishna
Eckloff, Bruce
Baral, Aradhita
Singh, Ankita
Halder, Rashi
Kumar, Akinchan
Alam, Mohammad Parwez
Kundu, Tapas K.
Pandita, Raj
Pandita, Tej K.
Wieben, Eric D.
Chowdhury, Shantanu
author_facet Yadav, Vinod Kumar
Thakur, Ram Krishna
Eckloff, Bruce
Baral, Aradhita
Singh, Ankita
Halder, Rashi
Kumar, Akinchan
Alam, Mohammad Parwez
Kundu, Tapas K.
Pandita, Raj
Pandita, Tej K.
Wieben, Eric D.
Chowdhury, Shantanu
author_sort Yadav, Vinod Kumar
collection PubMed
description Previous studies have analyzed patterns of transcription, transcription factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown. For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF. Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression? With these in mind, following characterization of two states (before and after induction of a single TF of choice) we determined: (i) genomic binding sites of the TF, (ii) promoter nucleosome occupancy and (iii) transcriptome profiles. Results demonstrated that promoter-proximal TF binding influenced expression of the target gene when it was coupled to nucleosome repositioning at or close to its binding site in most cases. In contrast, only in few cases change in target gene expression was found when TF binding occurred without local nucleosome reorganization.
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spelling pubmed-41507652014-12-01 Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity Yadav, Vinod Kumar Thakur, Ram Krishna Eckloff, Bruce Baral, Aradhita Singh, Ankita Halder, Rashi Kumar, Akinchan Alam, Mohammad Parwez Kundu, Tapas K. Pandita, Raj Pandita, Tej K. Wieben, Eric D. Chowdhury, Shantanu Nucleic Acids Res Gene regulation, Chromatin and Epigenetics Previous studies have analyzed patterns of transcription, transcription factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown. For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF. Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression? With these in mind, following characterization of two states (before and after induction of a single TF of choice) we determined: (i) genomic binding sites of the TF, (ii) promoter nucleosome occupancy and (iii) transcriptome profiles. Results demonstrated that promoter-proximal TF binding influenced expression of the target gene when it was coupled to nucleosome repositioning at or close to its binding site in most cases. In contrast, only in few cases change in target gene expression was found when TF binding occurred without local nucleosome reorganization. Oxford University Press 2014-09-02 2014-07-31 /pmc/articles/PMC4150765/ /pubmed/25081206 http://dx.doi.org/10.1093/nar/gku596 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Gene regulation, Chromatin and Epigenetics
Yadav, Vinod Kumar
Thakur, Ram Krishna
Eckloff, Bruce
Baral, Aradhita
Singh, Ankita
Halder, Rashi
Kumar, Akinchan
Alam, Mohammad Parwez
Kundu, Tapas K.
Pandita, Raj
Pandita, Tej K.
Wieben, Eric D.
Chowdhury, Shantanu
Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
title Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
title_full Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
title_fullStr Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
title_full_unstemmed Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
title_short Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
title_sort promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity
topic Gene regulation, Chromatin and Epigenetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150765/
https://www.ncbi.nlm.nih.gov/pubmed/25081206
http://dx.doi.org/10.1093/nar/gku596
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