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A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions

Cellular homeostasis requires the orderly expression of thousands of transcripts. Gene expression is regulated by numerous proteins that recognize post-translational modifications—in particular, the acetylation of lysine residues (Kac) on histones. In addition to affecting the general condensation s...

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Autores principales: Loehr, Jérémy, Kougnassoukou Tchara, Pata-Eting, Gonthier, Kevin, Noufi, Chahinez, Linteau, Naomie, Audet-Walsh, Étienne, Lambert, Jean-Philippe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8984119/
https://www.ncbi.nlm.nih.gov/pubmed/35402505
http://dx.doi.org/10.3389/fmolb.2022.831758
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author Loehr, Jérémy
Kougnassoukou Tchara, Pata-Eting
Gonthier, Kevin
Noufi, Chahinez
Linteau, Naomie
Audet-Walsh, Étienne
Lambert, Jean-Philippe
author_facet Loehr, Jérémy
Kougnassoukou Tchara, Pata-Eting
Gonthier, Kevin
Noufi, Chahinez
Linteau, Naomie
Audet-Walsh, Étienne
Lambert, Jean-Philippe
author_sort Loehr, Jérémy
collection PubMed
description Cellular homeostasis requires the orderly expression of thousands of transcripts. Gene expression is regulated by numerous proteins that recognize post-translational modifications—in particular, the acetylation of lysine residues (Kac) on histones. In addition to affecting the general condensation state of the chromatin, acetylated histones act as anchor points for bromodomain (BRD)-containing adapter proteins. BRDs are the primary Kac reader domains in humans, and proteins containing them act as chromatin scaffolds that organize large networks of interactions to regulate transcription. To characterize BRD-dependent interaction networks, we established cell lines in which histone acetylation is dependent on acetate supplementation. To do this, we used genome editing to knock out ATP citrate lyase (ACLY), the enzyme responsible for converting citrate to oxaloacetate and acetyl-CoA in the cytoplasm and nucleus. In our cellular model, removing acetate from the culture medium resulted in the rapid catabolism of acetylated histones to restore the nucleocytoplasmic acetyl-CoA pool. Here we report the use of our new model in functional proteomics studies to characterize BRD-dependent interaction networks on the chromatin.
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spelling pubmed-89841192022-04-07 A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions Loehr, Jérémy Kougnassoukou Tchara, Pata-Eting Gonthier, Kevin Noufi, Chahinez Linteau, Naomie Audet-Walsh, Étienne Lambert, Jean-Philippe Front Mol Biosci Molecular Biosciences Cellular homeostasis requires the orderly expression of thousands of transcripts. Gene expression is regulated by numerous proteins that recognize post-translational modifications—in particular, the acetylation of lysine residues (Kac) on histones. In addition to affecting the general condensation state of the chromatin, acetylated histones act as anchor points for bromodomain (BRD)-containing adapter proteins. BRDs are the primary Kac reader domains in humans, and proteins containing them act as chromatin scaffolds that organize large networks of interactions to regulate transcription. To characterize BRD-dependent interaction networks, we established cell lines in which histone acetylation is dependent on acetate supplementation. To do this, we used genome editing to knock out ATP citrate lyase (ACLY), the enzyme responsible for converting citrate to oxaloacetate and acetyl-CoA in the cytoplasm and nucleus. In our cellular model, removing acetate from the culture medium resulted in the rapid catabolism of acetylated histones to restore the nucleocytoplasmic acetyl-CoA pool. Here we report the use of our new model in functional proteomics studies to characterize BRD-dependent interaction networks on the chromatin. Frontiers Media S.A. 2022-03-23 /pmc/articles/PMC8984119/ /pubmed/35402505 http://dx.doi.org/10.3389/fmolb.2022.831758 Text en Copyright © 2022 Loehr, Kougnassoukou Tchara, Gonthier, Noufi, Linteau, Audet-Walsh and Lambert. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Loehr, Jérémy
Kougnassoukou Tchara, Pata-Eting
Gonthier, Kevin
Noufi, Chahinez
Linteau, Naomie
Audet-Walsh, Étienne
Lambert, Jean-Philippe
A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions
title A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions
title_full A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions
title_fullStr A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions
title_full_unstemmed A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions
title_short A Nutrient-Based Cellular Model to Characterize Acetylation-Dependent Protein-Protein Interactions
title_sort nutrient-based cellular model to characterize acetylation-dependent protein-protein interactions
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8984119/
https://www.ncbi.nlm.nih.gov/pubmed/35402505
http://dx.doi.org/10.3389/fmolb.2022.831758
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