Enhancer regions show high histone H3.3 turnover that changes during differentiation
The organization of DNA into chromatin is dynamic; nucleosomes are frequently displaced to facilitate the ability of regulatory proteins to access specific DNA elements. To gain insight into nucleosome dynamics, and to follow how dynamics change during differentiation, we used a technique called tim...
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doaj-ece94af87bd149a69da91605cfc44b1a2021-05-05T00:26:42ZengeLife Sciences Publications LtdeLife2050-084X2016-06-01510.7554/eLife.15316Enhancer regions show high histone H3.3 turnover that changes during differentiationAimee M Deaton0Mariluz Gómez-Rodríguez1Jakub Mieczkowski2Michael Y Tolstorukov3Sharmistha Kundu4Ruslan I Sadreyev5Lars ET Jansen6Robert E Kingston7https://orcid.org/0000-0003-3628-4335Department of Molecular Biology, Massachusetts General Hospital, Boston, United States; Department of Genetics, Harvard Medical School, Boston, United StatesLaboratory for Epigenetic Mechanisms, Instituto Gulbenkian de Ciencia, Oeiras, PortugalDepartment of Molecular Biology, Massachusetts General Hospital, Boston, United States; Department of Genetics, Harvard Medical School, Boston, United StatesDepartment of Molecular Biology, Massachusetts General Hospital, Boston, United States; Department of Medicine, Harvard Medical School, Boston, United StatesDepartment of Molecular Biology, Massachusetts General Hospital, Boston, United States; Department of Genetics, Harvard Medical School, Boston, United StatesDepartment of Molecular Biology, Massachusetts General Hospital, Boston, United States; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, United StatesLaboratory for Epigenetic Mechanisms, Instituto Gulbenkian de Ciencia, Oeiras, PortugalDepartment of Molecular Biology, Massachusetts General Hospital, Boston, United States; Department of Genetics, Harvard Medical School, Boston, United StatesThe organization of DNA into chromatin is dynamic; nucleosomes are frequently displaced to facilitate the ability of regulatory proteins to access specific DNA elements. To gain insight into nucleosome dynamics, and to follow how dynamics change during differentiation, we used a technique called time-ChIP to quantitatively assess histone H3.3 turnover genome-wide during differentiation of mouse ESCs. We found that, without prior assumptions, high turnover could be used to identify regions involved in gene regulation. High turnover was seen at enhancers, as observed previously, with particularly high turnover at super-enhancers. In contrast, regions associated with the repressive Polycomb-Group showed low turnover in ESCs. Turnover correlated with DNA accessibility. Upon differentiation, numerous changes in H3.3 turnover rates were observed, the majority of which occurred at enhancers. Thus, time-ChIP measurement of histone turnover shows that active enhancers are unusually dynamic in ESCs and changes in highly dynamic nucleosomes predominate at enhancers during differentiation.https://elifesciences.org/articles/15316chromatinhistone H3.3turnoverdifferentiationstem cells |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Aimee M Deaton Mariluz Gómez-Rodríguez Jakub Mieczkowski Michael Y Tolstorukov Sharmistha Kundu Ruslan I Sadreyev Lars ET Jansen Robert E Kingston |
spellingShingle |
Aimee M Deaton Mariluz Gómez-Rodríguez Jakub Mieczkowski Michael Y Tolstorukov Sharmistha Kundu Ruslan I Sadreyev Lars ET Jansen Robert E Kingston Enhancer regions show high histone H3.3 turnover that changes during differentiation eLife chromatin histone H3.3 turnover differentiation stem cells |
author_facet |
Aimee M Deaton Mariluz Gómez-Rodríguez Jakub Mieczkowski Michael Y Tolstorukov Sharmistha Kundu Ruslan I Sadreyev Lars ET Jansen Robert E Kingston |
author_sort |
Aimee M Deaton |
title |
Enhancer regions show high histone H3.3 turnover that changes during differentiation |
title_short |
Enhancer regions show high histone H3.3 turnover that changes during differentiation |
title_full |
Enhancer regions show high histone H3.3 turnover that changes during differentiation |
title_fullStr |
Enhancer regions show high histone H3.3 turnover that changes during differentiation |
title_full_unstemmed |
Enhancer regions show high histone H3.3 turnover that changes during differentiation |
title_sort |
enhancer regions show high histone h3.3 turnover that changes during differentiation |
publisher |
eLife Sciences Publications Ltd |
series |
eLife |
issn |
2050-084X |
publishDate |
2016-06-01 |
description |
The organization of DNA into chromatin is dynamic; nucleosomes are frequently displaced to facilitate the ability of regulatory proteins to access specific DNA elements. To gain insight into nucleosome dynamics, and to follow how dynamics change during differentiation, we used a technique called time-ChIP to quantitatively assess histone H3.3 turnover genome-wide during differentiation of mouse ESCs. We found that, without prior assumptions, high turnover could be used to identify regions involved in gene regulation. High turnover was seen at enhancers, as observed previously, with particularly high turnover at super-enhancers. In contrast, regions associated with the repressive Polycomb-Group showed low turnover in ESCs. Turnover correlated with DNA accessibility. Upon differentiation, numerous changes in H3.3 turnover rates were observed, the majority of which occurred at enhancers. Thus, time-ChIP measurement of histone turnover shows that active enhancers are unusually dynamic in ESCs and changes in highly dynamic nucleosomes predominate at enhancers during differentiation. |
topic |
chromatin histone H3.3 turnover differentiation stem cells |
url |
https://elifesciences.org/articles/15316 |
work_keys_str_mv |
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