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TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity

Despite overwhelming evidence that transcriptional activation by TP53 is critical for its tumor suppressive activity, the mechanisms by which TP53 engages the genome in the context of chromatin to activate transcription are not well understood. Using a compendium of novel and existing genome-wide da...

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Autores principales: Sammons, Morgan A., Zhu, Jiajun, Drake, Adam M., Berger, Shelley L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315292/
https://www.ncbi.nlm.nih.gov/pubmed/25391375
http://dx.doi.org/10.1101/gr.181883.114
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author Sammons, Morgan A.
Zhu, Jiajun
Drake, Adam M.
Berger, Shelley L.
author_facet Sammons, Morgan A.
Zhu, Jiajun
Drake, Adam M.
Berger, Shelley L.
author_sort Sammons, Morgan A.
collection PubMed
description Despite overwhelming evidence that transcriptional activation by TP53 is critical for its tumor suppressive activity, the mechanisms by which TP53 engages the genome in the context of chromatin to activate transcription are not well understood. Using a compendium of novel and existing genome-wide data sets, we examined the relationship between TP53 binding and the dynamics of the local chromatin environment. Our analysis revealed three distinct categories of TP53 binding events that differ based on the dynamics of the local chromatin environment. The first class of TP53 binding events occurs near transcriptional start sites (TSS) and is defined by previously characterized promoter-associated chromatin modifications. The second class comprises a large cohort of preestablished, promoter-distal enhancer elements that demonstrates dynamic histone acetylation and transcription upon TP53 binding. The third class of TP53 binding sites is devoid of classic chromatin modifications and, remarkably, fall within regions of inaccessible chromatin, suggesting that TP53 has intrinsic pioneer factor activity and binds within structurally inaccessible regions of chromatin. Intriguingly, these inaccessible TP53 binding sites feature several enhancer-like properties in cell types within the epithelial lineage, indicating that TP53 binding events include a group of “proto-enhancers” that become active enhancers given the appropriate cellular context. These data indicate that TP53, along with TP63, may act as pioneer factors to specify epithelial enhancers. Further, these findings suggest that rather than following a global cell-type invariant stress response program, TP53 may tune its response based on the lineage-specific epigenomic landscape.
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spelling pubmed-43152922015-08-01 TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity Sammons, Morgan A. Zhu, Jiajun Drake, Adam M. Berger, Shelley L. Genome Res Research Despite overwhelming evidence that transcriptional activation by TP53 is critical for its tumor suppressive activity, the mechanisms by which TP53 engages the genome in the context of chromatin to activate transcription are not well understood. Using a compendium of novel and existing genome-wide data sets, we examined the relationship between TP53 binding and the dynamics of the local chromatin environment. Our analysis revealed three distinct categories of TP53 binding events that differ based on the dynamics of the local chromatin environment. The first class of TP53 binding events occurs near transcriptional start sites (TSS) and is defined by previously characterized promoter-associated chromatin modifications. The second class comprises a large cohort of preestablished, promoter-distal enhancer elements that demonstrates dynamic histone acetylation and transcription upon TP53 binding. The third class of TP53 binding sites is devoid of classic chromatin modifications and, remarkably, fall within regions of inaccessible chromatin, suggesting that TP53 has intrinsic pioneer factor activity and binds within structurally inaccessible regions of chromatin. Intriguingly, these inaccessible TP53 binding sites feature several enhancer-like properties in cell types within the epithelial lineage, indicating that TP53 binding events include a group of “proto-enhancers” that become active enhancers given the appropriate cellular context. These data indicate that TP53, along with TP63, may act as pioneer factors to specify epithelial enhancers. Further, these findings suggest that rather than following a global cell-type invariant stress response program, TP53 may tune its response based on the lineage-specific epigenomic landscape. Cold Spring Harbor Laboratory Press 2015-02 /pmc/articles/PMC4315292/ /pubmed/25391375 http://dx.doi.org/10.1101/gr.181883.114 Text en © 2015 Sammons et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Sammons, Morgan A.
Zhu, Jiajun
Drake, Adam M.
Berger, Shelley L.
TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
title TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
title_full TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
title_fullStr TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
title_full_unstemmed TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
title_short TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
title_sort tp53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315292/
https://www.ncbi.nlm.nih.gov/pubmed/25391375
http://dx.doi.org/10.1101/gr.181883.114
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