Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data

Abstract In the study of genomic regulation, strategies to integrate the data produced by Next Generation Sequencing (NGS)-based technologies in a meaningful ensemble are eagerly awaited and must continuously evolve. Here, we describe an integrative strategy for the analysis of data generated by chr...

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Autores principales:	Giulio Ferrero, Valentina Miano, Marco Beccuti, Gianfranco Balbo, Michele De Bortoli, Francesca Cordero
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6499eef60fb94cbbacc08698c84a01ef
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spelling	oai:doaj.org-article:6499eef60fb94cbbacc08698c84a01ef2021-12-02T12:32:46ZDissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data10.1038/s41598-017-08754-92045-2322https://doaj.org/article/6499eef60fb94cbbacc08698c84a01ef2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08754-9https://doaj.org/toc/2045-2322Abstract In the study of genomic regulation, strategies to integrate the data produced by Next Generation Sequencing (NGS)-based technologies in a meaningful ensemble are eagerly awaited and must continuously evolve. Here, we describe an integrative strategy for the analysis of data generated by chromatin immunoprecipitation followed by NGS which combines algorithms for data overlap, normalization and epigenetic state analysis. The performance of our strategy is illustrated by presenting the analysis of data relative to the transcriptional regulator Estrogen Receptor alpha (ERα) in MCF-7 breast cancer cells and of Glucocorticoid Receptor (GR) in A549 lung cancer cells. We went through the definition of reference cistromes for different experimental contexts, the integration of data relative to co-regulators and the overlay of chromatin states as defined by epigenetic marks in MCF-7 cells. With our strategy, we identified novel features of estrogen-independent ERα activity, including FoxM1 interaction, eRNAs transcription and a peculiar ontology of connected genes.Giulio FerreroValentina MianoMarco BeccutiGianfranco BalboMichele De BortoliFrancesca CorderoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Giulio Ferrero Valentina Miano Marco Beccuti Gianfranco Balbo Michele De Bortoli Francesca Cordero Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
description	Abstract In the study of genomic regulation, strategies to integrate the data produced by Next Generation Sequencing (NGS)-based technologies in a meaningful ensemble are eagerly awaited and must continuously evolve. Here, we describe an integrative strategy for the analysis of data generated by chromatin immunoprecipitation followed by NGS which combines algorithms for data overlap, normalization and epigenetic state analysis. The performance of our strategy is illustrated by presenting the analysis of data relative to the transcriptional regulator Estrogen Receptor alpha (ERα) in MCF-7 breast cancer cells and of Glucocorticoid Receptor (GR) in A549 lung cancer cells. We went through the definition of reference cistromes for different experimental contexts, the integration of data relative to co-regulators and the overlay of chromatin states as defined by epigenetic marks in MCF-7 cells. With our strategy, we identified novel features of estrogen-independent ERα activity, including FoxM1 interaction, eRNAs transcription and a peculiar ontology of connected genes.
format	article
author	Giulio Ferrero Valentina Miano Marco Beccuti Gianfranco Balbo Michele De Bortoli Francesca Cordero
author_facet	Giulio Ferrero Valentina Miano Marco Beccuti Gianfranco Balbo Michele De Bortoli Francesca Cordero
author_sort	Giulio Ferrero
title	Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
title_short	Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
title_full	Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
title_fullStr	Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
title_full_unstemmed	Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
title_sort	dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/6499eef60fb94cbbacc08698c84a01ef
work_keys_str_mv	AT giulioferrero dissectingthegenomicactivityofatranscriptionalregulatorbytheintegrativeanalysisofomicsdata AT valentinamiano dissectingthegenomicactivityofatranscriptionalregulatorbytheintegrativeanalysisofomicsdata AT marcobeccuti dissectingthegenomicactivityofatranscriptionalregulatorbytheintegrativeanalysisofomicsdata AT gianfrancobalbo dissectingthegenomicactivityofatranscriptionalregulatorbytheintegrativeanalysisofomicsdata AT micheledebortoli dissectingthegenomicactivityofatranscriptionalregulatorbytheintegrativeanalysisofomicsdata AT francescacordero dissectingthegenomicactivityofatranscriptionalregulatorbytheintegrativeanalysisofomicsdata
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Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data

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