CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

During development eukaryotic gene expression is coordinated by dynamic changes in chromatin structure. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibi...

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Main Authors: Gabriel N Aughey, Alicia Estacio Gomez, Jamie Thomson, Hang Yin, Tony D Southall
Format: Article
Language:English
Published: eLife Sciences Publications Ltd 2018-02-01
Series:eLife
Subjects:
Online Access:https://elifesciences.org/articles/32341
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spelling doaj-bd352654e2b54b73a315422bfae47a472021-05-05T15:37:22ZengeLife Sciences Publications LtdeLife2050-084X2018-02-01710.7554/eLife.32341CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivoGabriel N Aughey0https://orcid.org/0000-0001-5610-9345Alicia Estacio Gomez1Jamie Thomson2Hang Yin3Tony D Southall4https://orcid.org/0000-0002-8645-4198Department of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDuring development eukaryotic gene expression is coordinated by dynamic changes in chromatin structure. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibility changes in the development of somatic lineages are not well defined. Here we show that cell-specific chromatin accessibility data can be produced via ectopic expression of E. coli Dam methylase in vivo, without the requirement for cell-sorting (CATaDa). We have profiled chromatin accessibility in individual cell-types of Drosophila neural and midgut lineages. Functional cell-type-specific enhancers were identified, as well as novel motifs enriched at different stages of development. Finally, we show global changes in the accessibility of chromatin between stem-cells and their differentiated progeny. Our results demonstrate the dynamic nature of chromatin accessibility in somatic tissues during stem cell differentiation and provide a novel approach to understanding gene regulatory mechanisms underlying development.https://elifesciences.org/articles/32341chromatin accessibilityneural developmentdifferentiation
collection DOAJ
language English
format Article
sources DOAJ
author Gabriel N Aughey
Alicia Estacio Gomez
Jamie Thomson
Hang Yin
Tony D Southall
spellingShingle Gabriel N Aughey
Alicia Estacio Gomez
Jamie Thomson
Hang Yin
Tony D Southall
CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
eLife
chromatin accessibility
neural development
differentiation
author_facet Gabriel N Aughey
Alicia Estacio Gomez
Jamie Thomson
Hang Yin
Tony D Southall
author_sort Gabriel N Aughey
title CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_short CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_full CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_fullStr CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_full_unstemmed CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_sort catada reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
publisher eLife Sciences Publications Ltd
series eLife
issn 2050-084X
publishDate 2018-02-01
description During development eukaryotic gene expression is coordinated by dynamic changes in chromatin structure. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibility changes in the development of somatic lineages are not well defined. Here we show that cell-specific chromatin accessibility data can be produced via ectopic expression of E. coli Dam methylase in vivo, without the requirement for cell-sorting (CATaDa). We have profiled chromatin accessibility in individual cell-types of Drosophila neural and midgut lineages. Functional cell-type-specific enhancers were identified, as well as novel motifs enriched at different stages of development. Finally, we show global changes in the accessibility of chromatin between stem-cells and their differentiated progeny. Our results demonstrate the dynamic nature of chromatin accessibility in somatic tissues during stem cell differentiation and provide a novel approach to understanding gene regulatory mechanisms underlying development.
topic chromatin accessibility
neural development
differentiation
url https://elifesciences.org/articles/32341
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