Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

ABSTRACT To build transcription regulatory networks, transcription factor binding must be analyzed in cells grown under different conditions because their responses and targets differ depending on environmental conditions. We performed whole-genome analysis of the DNA binding of five Saccharomyces c...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	David Bergenholm, Guodong Liu, Petter Holland, Jens Nielsen
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	ChIP-exo transcriptional regulatory network environmental response lipid metabolic map novel targets Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b3b0bc78d88f4d9d9f00106bdcdb04ff
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b3b0bc78d88f4d9d9f00106bdcdb04ff
record_format	dspace
spelling	oai:doaj.org-article:b3b0bc78d88f4d9d9f00106bdcdb04ff2021-12-02T19:45:30ZReconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion10.1128/mSystems.00215-172379-5077https://doaj.org/article/b3b0bc78d88f4d9d9f00106bdcdb04ff2018-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00215-17https://doaj.org/toc/2379-5077ABSTRACT To build transcription regulatory networks, transcription factor binding must be analyzed in cells grown under different conditions because their responses and targets differ depending on environmental conditions. We performed whole-genome analysis of the DNA binding of five Saccharomyces cerevisiae transcription factors involved in lipid metabolism, Ino2, Ino4, Hap1, Oaf1, and Pip2, in response to four different environmental conditions in chemostat cultures, which allowed us to keep the specific growth rate constant. Chromatin immunoprecipitation with lambda exonuclease digestion (ChIP-exo) enabled the detection of binding events at a high resolution. We discovered a large number of unidentified targets and thus expanded functions for each transcription factor (e.g., glutamate biosynthesis as a target of Oaf1 and Pip2). Moreover, condition-dependent binding of transcription factors in response to cell metabolic state (e.g., differential binding of Ino2 between fermentative and respiratory metabolic conditions) was clearly suggested. Combining the new binding data with previously published data from transcription factor deletion studies revealed the high complexity of the transcriptional regulatory network for lipid metabolism in yeast, which involves the combinatorial and complementary regulation by multiple transcription factors. We anticipate that our work will provide insights into transcription factor binding dynamics that will prove useful for the understanding of transcription regulatory networks. IMPORTANCE Transcription factors play a crucial role in the regulation of gene expression and adaptation to different environments. To better understand the underlying roles of these adaptations, we performed experiments that give us high-resolution binding of transcription factors to their targets. We investigated five transcription factors involved in lipid metabolism in yeast, and we discovered multiple novel targets and condition-specific responses that allow us to draw a better regulatory map of the lipid metabolism.David BergenholmGuodong LiuPetter HollandJens NielsenAmerican Society for MicrobiologyarticleChIP-exotranscriptional regulatory networkenvironmental responselipid metabolic mapnovel targetsMicrobiologyQR1-502ENmSystems, Vol 3, Iss 4 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	ChIP-exo transcriptional regulatory network environmental response lipid metabolic map novel targets Microbiology QR1-502
spellingShingle	ChIP-exo transcriptional regulatory network environmental response lipid metabolic map novel targets Microbiology QR1-502 David Bergenholm Guodong Liu Petter Holland Jens Nielsen Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
description	ABSTRACT To build transcription regulatory networks, transcription factor binding must be analyzed in cells grown under different conditions because their responses and targets differ depending on environmental conditions. We performed whole-genome analysis of the DNA binding of five Saccharomyces cerevisiae transcription factors involved in lipid metabolism, Ino2, Ino4, Hap1, Oaf1, and Pip2, in response to four different environmental conditions in chemostat cultures, which allowed us to keep the specific growth rate constant. Chromatin immunoprecipitation with lambda exonuclease digestion (ChIP-exo) enabled the detection of binding events at a high resolution. We discovered a large number of unidentified targets and thus expanded functions for each transcription factor (e.g., glutamate biosynthesis as a target of Oaf1 and Pip2). Moreover, condition-dependent binding of transcription factors in response to cell metabolic state (e.g., differential binding of Ino2 between fermentative and respiratory metabolic conditions) was clearly suggested. Combining the new binding data with previously published data from transcription factor deletion studies revealed the high complexity of the transcriptional regulatory network for lipid metabolism in yeast, which involves the combinatorial and complementary regulation by multiple transcription factors. We anticipate that our work will provide insights into transcription factor binding dynamics that will prove useful for the understanding of transcription regulatory networks. IMPORTANCE Transcription factors play a crucial role in the regulation of gene expression and adaptation to different environments. To better understand the underlying roles of these adaptations, we performed experiments that give us high-resolution binding of transcription factors to their targets. We investigated five transcription factors involved in lipid metabolism in yeast, and we discovered multiple novel targets and condition-specific responses that allow us to draw a better regulatory map of the lipid metabolism.
format	article
author	David Bergenholm Guodong Liu Petter Holland Jens Nielsen
author_facet	David Bergenholm Guodong Liu Petter Holland Jens Nielsen
author_sort	David Bergenholm
title	Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
title_short	Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
title_full	Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
title_fullStr	Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
title_full_unstemmed	Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
title_sort	reconstruction of a global transcriptional regulatory network for control of lipid metabolism in yeast by using chromatin immunoprecipitation with lambda exonuclease digestion
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/b3b0bc78d88f4d9d9f00106bdcdb04ff
work_keys_str_mv	AT davidbergenholm reconstructionofaglobaltranscriptionalregulatorynetworkforcontroloflipidmetabolisminyeastbyusingchromatinimmunoprecipitationwithlambdaexonucleasedigestion AT guodongliu reconstructionofaglobaltranscriptionalregulatorynetworkforcontroloflipidmetabolisminyeastbyusingchromatinimmunoprecipitationwithlambdaexonucleasedigestion AT petterholland reconstructionofaglobaltranscriptionalregulatorynetworkforcontroloflipidmetabolisminyeastbyusingchromatinimmunoprecipitationwithlambdaexonucleasedigestion AT jensnielsen reconstructionofaglobaltranscriptionalregulatorynetworkforcontroloflipidmetabolisminyeastbyusingchromatinimmunoprecipitationwithlambdaexonucleasedigestion
_version_	1718376046432092160

Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

Ejemplares similares