Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies

Abstract The collection of known posttranslational modifications (PTMs) has expanded rapidly with the identification of various non-acetyl histone lysine acylations, such as crotonylation, succinylation and butyrylation, yet their regulation is still not fully understood. Through an unbiased chromat...

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Autores principales:	Leonie Kollenstart, Sophie C. van der Horst, Kees Vreeken, George M. C. Janssen, Fabrizio Martino, Hanneke Vlaming, Peter A. van Veelen, Fred van Leeuwen, Haico van Attikum
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/49d63814a9b84605a12502b41eee17ad
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spelling	oai:doaj.org-article:49d63814a9b84605a12502b41eee17ad2021-12-02T17:24:09ZEpigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies10.1038/s41598-021-91359-02045-2322https://doaj.org/article/49d63814a9b84605a12502b41eee17ad2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91359-0https://doaj.org/toc/2045-2322Abstract The collection of known posttranslational modifications (PTMs) has expanded rapidly with the identification of various non-acetyl histone lysine acylations, such as crotonylation, succinylation and butyrylation, yet their regulation is still not fully understood. Through an unbiased chromatin immunoprecipitation (ChIP)-based approach called Epigenetics-IDentifier (Epi-ID), we aimed to identify regulators of crotonylation, succinylation and butyrylation in thousands of yeast mutants simultaneously. However, highly correlative results led us to further investigate the specificity of the pan-K-acyl antibodies used in our Epi-ID studies. This revealed cross-reactivity and lack of specificity of pan-K-acyl antibodies in various assays. Our findings suggest that the antibodies might recognize histone acetylation in vivo, in addition to histone acylation, due to the vast overabundance of acetylation compared to other acylation modifications in cells. Consequently, our Epi-ID screen mostly identified factors affecting histone acetylation, including known (e.g. GCN5, HDA1, and HDA2) and unanticipated (MET7, MTF1, CLB3, and RAD26) factors, expanding the repertoire of acetylation regulators. Antibody-independent follow-up experiments on the Gcn5-Ada2-Ada3 (ADA) complex revealed that, in addition to acetylation and crotonylation, ADA has the ability to butyrylate histones. Thus, our Epi-ID screens revealed limits of using pan-K-acyl antibodies in epigenetics research, expanded the repertoire of regulators of histone acetylation, and attributed butyrylation activity to the ADA complex.Leonie KollenstartSophie C. van der HorstKees VreekenGeorge M. C. JanssenFabrizio MartinoHanneke VlamingPeter A. van VeelenFred van LeeuwenHaico van AttikumNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Leonie Kollenstart Sophie C. van der Horst Kees Vreeken George M. C. Janssen Fabrizio Martino Hanneke Vlaming Peter A. van Veelen Fred van Leeuwen Haico van Attikum Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
description	Abstract The collection of known posttranslational modifications (PTMs) has expanded rapidly with the identification of various non-acetyl histone lysine acylations, such as crotonylation, succinylation and butyrylation, yet their regulation is still not fully understood. Through an unbiased chromatin immunoprecipitation (ChIP)-based approach called Epigenetics-IDentifier (Epi-ID), we aimed to identify regulators of crotonylation, succinylation and butyrylation in thousands of yeast mutants simultaneously. However, highly correlative results led us to further investigate the specificity of the pan-K-acyl antibodies used in our Epi-ID studies. This revealed cross-reactivity and lack of specificity of pan-K-acyl antibodies in various assays. Our findings suggest that the antibodies might recognize histone acetylation in vivo, in addition to histone acylation, due to the vast overabundance of acetylation compared to other acylation modifications in cells. Consequently, our Epi-ID screen mostly identified factors affecting histone acetylation, including known (e.g. GCN5, HDA1, and HDA2) and unanticipated (MET7, MTF1, CLB3, and RAD26) factors, expanding the repertoire of acetylation regulators. Antibody-independent follow-up experiments on the Gcn5-Ada2-Ada3 (ADA) complex revealed that, in addition to acetylation and crotonylation, ADA has the ability to butyrylate histones. Thus, our Epi-ID screens revealed limits of using pan-K-acyl antibodies in epigenetics research, expanded the repertoire of regulators of histone acetylation, and attributed butyrylation activity to the ADA complex.
format	article
author	Leonie Kollenstart Sophie C. van der Horst Kees Vreeken George M. C. Janssen Fabrizio Martino Hanneke Vlaming Peter A. van Veelen Fred van Leeuwen Haico van Attikum
author_facet	Leonie Kollenstart Sophie C. van der Horst Kees Vreeken George M. C. Janssen Fabrizio Martino Hanneke Vlaming Peter A. van Veelen Fred van Leeuwen Haico van Attikum
author_sort	Leonie Kollenstart
title	Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
title_short	Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
title_full	Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
title_fullStr	Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
title_full_unstemmed	Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
title_sort	epigenetics identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/49d63814a9b84605a12502b41eee17ad
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Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies

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