Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.

Muscle cells have different phenotypes adapted to different usage, and can be grossly divided into fast/glycolytic and slow/oxidative types. While most muscles contain a mixture of such fiber types, we aimed at providing a genome-wide analysis of the epigenetic landscape by ChIP-Seq in two muscle ex...

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Autores principales:	Mads Bengtsen, Ivan Myhre Winje, Einar Eftestøl, Johannes Landskron, Chengyi Sun, Kamilla Nygård, Diana Domanska, Douglas P Millay, Leonardo A Meza-Zepeda, Kristian Gundersen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/c5a59212ff0d45498966814afcc41998
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spelling	oai:doaj.org-article:c5a59212ff0d45498966814afcc419982021-12-02T20:03:15ZComparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.1553-73901553-740410.1371/journal.pgen.1009907https://doaj.org/article/c5a59212ff0d45498966814afcc419982021-11-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009907https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Muscle cells have different phenotypes adapted to different usage, and can be grossly divided into fast/glycolytic and slow/oxidative types. While most muscles contain a mixture of such fiber types, we aimed at providing a genome-wide analysis of the epigenetic landscape by ChIP-Seq in two muscle extremes, the fast/glycolytic extensor digitorum longus (EDL) and slow/oxidative soleus muscles. Muscle is a heterogeneous tissue where up to 60% of the nuclei can be of a different origin. Since cellular homogeneity is critical in epigenome-wide association studies we developed a new method for purifying skeletal muscle nuclei from whole tissue, based on the nuclear envelope protein Pericentriolar material 1 (PCM1) being a specific marker for myonuclei. Using antibody labelling and a magnetic-assisted sorting approach, we were able to sort out myonuclei with 95% purity in muscles from mice, rats and humans. The sorting eliminated influence from the other cell types in the tissue and improved the myo-specific signal. A genome-wide comparison of the epigenetic landscape in EDL and soleus reflected the differences in the functional properties of the two muscles, and revealed distinct regulatory programs involving distal enhancers, including a glycolytic super-enhancer in the EDL. The two muscles were also regulated by different sets of transcription factors; e.g. in soleus, binding sites for MEF2C, NFATC2 and PPARA were enriched, while in EDL MYOD1 and SIX1 binding sites were found to be overrepresented. In addition, more novel transcription factors for muscle regulation such as members of the MAF family, ZFX and ZBTB14 were identified.Mads BengtsenIvan Myhre WinjeEinar EftestølJohannes LandskronChengyi SunKamilla NygårdDiana DomanskaDouglas P MillayLeonardo A Meza-ZepedaKristian GundersenPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 11, p e1009907 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Mads Bengtsen Ivan Myhre Winje Einar Eftestøl Johannes Landskron Chengyi Sun Kamilla Nygård Diana Domanska Douglas P Millay Leonardo A Meza-Zepeda Kristian Gundersen Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.
description	Muscle cells have different phenotypes adapted to different usage, and can be grossly divided into fast/glycolytic and slow/oxidative types. While most muscles contain a mixture of such fiber types, we aimed at providing a genome-wide analysis of the epigenetic landscape by ChIP-Seq in two muscle extremes, the fast/glycolytic extensor digitorum longus (EDL) and slow/oxidative soleus muscles. Muscle is a heterogeneous tissue where up to 60% of the nuclei can be of a different origin. Since cellular homogeneity is critical in epigenome-wide association studies we developed a new method for purifying skeletal muscle nuclei from whole tissue, based on the nuclear envelope protein Pericentriolar material 1 (PCM1) being a specific marker for myonuclei. Using antibody labelling and a magnetic-assisted sorting approach, we were able to sort out myonuclei with 95% purity in muscles from mice, rats and humans. The sorting eliminated influence from the other cell types in the tissue and improved the myo-specific signal. A genome-wide comparison of the epigenetic landscape in EDL and soleus reflected the differences in the functional properties of the two muscles, and revealed distinct regulatory programs involving distal enhancers, including a glycolytic super-enhancer in the EDL. The two muscles were also regulated by different sets of transcription factors; e.g. in soleus, binding sites for MEF2C, NFATC2 and PPARA were enriched, while in EDL MYOD1 and SIX1 binding sites were found to be overrepresented. In addition, more novel transcription factors for muscle regulation such as members of the MAF family, ZFX and ZBTB14 were identified.
format	article
author	Mads Bengtsen Ivan Myhre Winje Einar Eftestøl Johannes Landskron Chengyi Sun Kamilla Nygård Diana Domanska Douglas P Millay Leonardo A Meza-Zepeda Kristian Gundersen
author_facet	Mads Bengtsen Ivan Myhre Winje Einar Eftestøl Johannes Landskron Chengyi Sun Kamilla Nygård Diana Domanska Douglas P Millay Leonardo A Meza-Zepeda Kristian Gundersen
author_sort	Mads Bengtsen
title	Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.
title_short	Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.
title_full	Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.
title_fullStr	Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.
title_full_unstemmed	Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.
title_sort	comparing the epigenetic landscape in myonuclei purified with a pcm1 antibody from a fast/glycolytic and a slow/oxidative muscle.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/c5a59212ff0d45498966814afcc41998
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Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle.

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