Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.

Metaboloepigenetics is a newly coined term in biological sciences that investigates the crosstalk between epigenetic modifications and metabolism. The reciprocal relation between biochemical transformations and gene expression regulation has been experimentally demonstrated in cancers and metabolic...

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Autores principales:	Ali Salehzadeh-Yazdi, Yazdan Asgari, Ali Akbar Saboury, Ali Masoudi-Nejad
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/38a2b9ea71d342759a38b625fbf097a1
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spelling	oai:doaj.org-article:38a2b9ea71d342759a38b625fbf097a12021-11-25T05:54:48ZComputational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.1932-620310.1371/journal.pone.0111686https://doaj.org/article/38a2b9ea71d342759a38b625fbf097a12014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0111686https://doaj.org/toc/1932-6203Metaboloepigenetics is a newly coined term in biological sciences that investigates the crosstalk between epigenetic modifications and metabolism. The reciprocal relation between biochemical transformations and gene expression regulation has been experimentally demonstrated in cancers and metabolic syndromes. In this study, we explored the metabolism-histone modifications crosstalk by topological analysis and constraint-based modeling approaches in the budding yeast. We constructed nine models through the integration of gene expression data of four mutated histone tails into a genome-scale metabolic model of yeast. Accordingly, we defined the centrality indices of the lowly expressed enzymes in the undirected enzyme-centric network of yeast by CytoHubba plug-in in Cytoscape. To determine the global effects of histone modifications on the yeast metabolism, the growth rate and the range of possible flux values of reactions, we used constraint-based modeling approach. Centrality analysis shows that the lowly expressed enzymes could affect and control the yeast metabolic network. Besides, constraint-based modeling results are in a good agreement with the experimental findings, confirming that the mutations in histone tails lead to non-lethal alterations in the yeast, but have diverse effects on the growth rate and reveal the functional redundancy.Ali Salehzadeh-YazdiYazdan AsgariAli Akbar SabouryAli Masoudi-NejadPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 11, p e111686 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ali Salehzadeh-Yazdi Yazdan Asgari Ali Akbar Saboury Ali Masoudi-Nejad Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.
description	Metaboloepigenetics is a newly coined term in biological sciences that investigates the crosstalk between epigenetic modifications and metabolism. The reciprocal relation between biochemical transformations and gene expression regulation has been experimentally demonstrated in cancers and metabolic syndromes. In this study, we explored the metabolism-histone modifications crosstalk by topological analysis and constraint-based modeling approaches in the budding yeast. We constructed nine models through the integration of gene expression data of four mutated histone tails into a genome-scale metabolic model of yeast. Accordingly, we defined the centrality indices of the lowly expressed enzymes in the undirected enzyme-centric network of yeast by CytoHubba plug-in in Cytoscape. To determine the global effects of histone modifications on the yeast metabolism, the growth rate and the range of possible flux values of reactions, we used constraint-based modeling approach. Centrality analysis shows that the lowly expressed enzymes could affect and control the yeast metabolic network. Besides, constraint-based modeling results are in a good agreement with the experimental findings, confirming that the mutations in histone tails lead to non-lethal alterations in the yeast, but have diverse effects on the growth rate and reveal the functional redundancy.
format	article
author	Ali Salehzadeh-Yazdi Yazdan Asgari Ali Akbar Saboury Ali Masoudi-Nejad
author_facet	Ali Salehzadeh-Yazdi Yazdan Asgari Ali Akbar Saboury Ali Masoudi-Nejad
author_sort	Ali Salehzadeh-Yazdi
title	Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.
title_short	Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.
title_full	Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.
title_fullStr	Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.
title_full_unstemmed	Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.
title_sort	computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (gsmm) approach.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/38a2b9ea71d342759a38b625fbf097a1
work_keys_str_mv	AT alisalehzadehyazdi computationalanalysisofreciprocalassociationofmetabolismandepigeneticsinthebuddingyeastagenomescalemetabolicmodelgsmmapproach AT yazdanasgari computationalanalysisofreciprocalassociationofmetabolismandepigeneticsinthebuddingyeastagenomescalemetabolicmodelgsmmapproach AT aliakbarsaboury computationalanalysisofreciprocalassociationofmetabolismandepigeneticsinthebuddingyeastagenomescalemetabolicmodelgsmmapproach AT alimasoudinejad computationalanalysisofreciprocalassociationofmetabolismandepigeneticsinthebuddingyeastagenomescalemetabolicmodelgsmmapproach
_version_	1718414392073125888

Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.

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