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Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach

The Yeast Metabolic Cycle (YMC) is a model system in which levels of around 60% of the yeast transcripts cycle over time. The spatial and temporal resolution provided by the YMC has revealed that changes in the yeast metabolic landscape and chromatin status can be related to cycling gene expression....

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Autores principales: Sánchez-Gaya, Víctor, Casaní-Galdón, Salvador, Ugidos, Manuel, Kuang, Zheng, Mellor, Jane, Conesa, Ana, Tarazona, Sonia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284056/
https://www.ncbi.nlm.nih.gov/pubmed/30555512
http://dx.doi.org/10.3389/fgene.2018.00578
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author Sánchez-Gaya, Víctor
Casaní-Galdón, Salvador
Ugidos, Manuel
Kuang, Zheng
Mellor, Jane
Conesa, Ana
Tarazona, Sonia
author_facet Sánchez-Gaya, Víctor
Casaní-Galdón, Salvador
Ugidos, Manuel
Kuang, Zheng
Mellor, Jane
Conesa, Ana
Tarazona, Sonia
author_sort Sánchez-Gaya, Víctor
collection PubMed
description The Yeast Metabolic Cycle (YMC) is a model system in which levels of around 60% of the yeast transcripts cycle over time. The spatial and temporal resolution provided by the YMC has revealed that changes in the yeast metabolic landscape and chromatin status can be related to cycling gene expression. However, the interplay between histone modifications and transcription factor activity during the YMC is still poorly understood. Here we apply an innovative statistical approach to integrate chromatin state (ChIP-seq) and gene expression (RNA-seq) data to investigate the transcriptional control during the YMC. By using the multivariate regression models N-PLS (Partial Least Squares) and MORE (Multi-Omics REgulation) methodologies, we assessed the contribution of histone marks and transcription factors to the regulation of gene expression in the YMC. We found that H3K18ac and H3K9ac were the most important histone modifications, whereas Sfp1, Hfi1, Pip2, Mig2, and Yhp1 emerged as the most relevant transcription factors. A significant association in the co-regulation of gene expression was found between H3K18ac and the transcription factors Pip2 (involved in fatty acids metabolism), Xbp1 (cyclin implicated in the regulation of carbohydrate and amino acid metabolism), and Hfi1 (involved in the formation of the SAGA complex). These results evidence the crucial role of histone lysine acetylation levels in the regulation of gene expression in the YMC through the coordinated action of transcription factors and lysine acetyltransferases.
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spelling pubmed-62840562018-12-14 Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach Sánchez-Gaya, Víctor Casaní-Galdón, Salvador Ugidos, Manuel Kuang, Zheng Mellor, Jane Conesa, Ana Tarazona, Sonia Front Genet Genetics The Yeast Metabolic Cycle (YMC) is a model system in which levels of around 60% of the yeast transcripts cycle over time. The spatial and temporal resolution provided by the YMC has revealed that changes in the yeast metabolic landscape and chromatin status can be related to cycling gene expression. However, the interplay between histone modifications and transcription factor activity during the YMC is still poorly understood. Here we apply an innovative statistical approach to integrate chromatin state (ChIP-seq) and gene expression (RNA-seq) data to investigate the transcriptional control during the YMC. By using the multivariate regression models N-PLS (Partial Least Squares) and MORE (Multi-Omics REgulation) methodologies, we assessed the contribution of histone marks and transcription factors to the regulation of gene expression in the YMC. We found that H3K18ac and H3K9ac were the most important histone modifications, whereas Sfp1, Hfi1, Pip2, Mig2, and Yhp1 emerged as the most relevant transcription factors. A significant association in the co-regulation of gene expression was found between H3K18ac and the transcription factors Pip2 (involved in fatty acids metabolism), Xbp1 (cyclin implicated in the regulation of carbohydrate and amino acid metabolism), and Hfi1 (involved in the formation of the SAGA complex). These results evidence the crucial role of histone lysine acetylation levels in the regulation of gene expression in the YMC through the coordinated action of transcription factors and lysine acetyltransferases. Frontiers Media S.A. 2018-11-30 /pmc/articles/PMC6284056/ /pubmed/30555512 http://dx.doi.org/10.3389/fgene.2018.00578 Text en Copyright © 2018 Sánchez-Gaya, Casaní-Galdón, Ugidos, Kuang, Mellor, Conesa and Tarazona. http://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 Genetics
Sánchez-Gaya, Víctor
Casaní-Galdón, Salvador
Ugidos, Manuel
Kuang, Zheng
Mellor, Jane
Conesa, Ana
Tarazona, Sonia
Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach
title Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach
title_full Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach
title_fullStr Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach
title_full_unstemmed Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach
title_short Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach
title_sort elucidating the role of chromatin state and transcription factors on the regulation of the yeast metabolic cycle: a multi-omic integrative approach
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284056/
https://www.ncbi.nlm.nih.gov/pubmed/30555512
http://dx.doi.org/10.3389/fgene.2018.00578
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