A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride

Botrytis cinerea and Trichoderma atroviride are two relevant fungi in agricultural systems. To gain insights into these organisms’ transcriptional gene regulatory networks (GRNs), we generated a manually curated transcription factor (TF) dataset for each of them, followed by a GRN inference utilizin...

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Autores principales:	Consuelo Olivares-Yañez, Evelyn Sánchez, Gabriel Pérez-Lara, Aldo Seguel, Pamela Y. Camejo, Luis F. Larrondo, Elena A. Vidal, Paulo Canessa
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Botrytis cinerea Trichoderma atroviride Transcription factors Gene Regulatory Network Mycoparasitism Biotechnology TP248.13-248.65
Acceso en línea:	https://doaj.org/article/fdc93badae7e426db0522535e53543f1
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spelling	oai:doaj.org-article:fdc93badae7e426db0522535e53543f12021-11-26T04:26:46ZA comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride2001-037010.1016/j.csbj.2021.11.012https://doaj.org/article/fdc93badae7e426db0522535e53543f12021-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2001037021004773https://doaj.org/toc/2001-0370Botrytis cinerea and Trichoderma atroviride are two relevant fungi in agricultural systems. To gain insights into these organisms’ transcriptional gene regulatory networks (GRNs), we generated a manually curated transcription factor (TF) dataset for each of them, followed by a GRN inference utilizing available sequence motifs describing DNA-binding specificity and global gene expression data. As a proof of concept of the usefulness of this resource to pinpoint key transcriptional regulators, we employed publicly available transcriptomics data and a newly generated dual RNA-seq dataset to build context-specific Botrytis and Trichoderma GRNs under two different biological paradigms: exposure to continuous light and Botrytis-Trichoderma confrontation assays. Network analysis of fungal responses to constant light revealed striking differences in the transcriptional landscape of both fungi. On the other hand, we found that the confrontation of both microorganisms elicited a distinct set of differentially expressed genes with changes in T. atroviride exceeding those in B. cinerea. Using our regulatory network data, we were able to determine, in both fungi, central TFs involved in this interaction response, including TFs controlling a large set of extracellular peptidases in the biocontrol agent T. atroviride. In summary, our work provides a comprehensive catalog of transcription factors and regulatory interactions for both organisms. This catalog can now serve as a basis for generating novel hypotheses on transcriptional regulatory circuits in different experimental contexts.Consuelo Olivares-YañezEvelyn SánchezGabriel Pérez-LaraAldo SeguelPamela Y. CamejoLuis F. LarrondoElena A. VidalPaulo CanessaElsevierarticleBotrytis cinereaTrichoderma atrovirideTranscription factorsGene Regulatory NetworkMycoparasitismBiotechnologyTP248.13-248.65ENComputational and Structural Biotechnology Journal, Vol 19, Iss , Pp 6212-6228 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Botrytis cinerea Trichoderma atroviride Transcription factors Gene Regulatory Network Mycoparasitism Biotechnology TP248.13-248.65
spellingShingle	Botrytis cinerea Trichoderma atroviride Transcription factors Gene Regulatory Network Mycoparasitism Biotechnology TP248.13-248.65 Consuelo Olivares-Yañez Evelyn Sánchez Gabriel Pérez-Lara Aldo Seguel Pamela Y. Camejo Luis F. Larrondo Elena A. Vidal Paulo Canessa A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
description	Botrytis cinerea and Trichoderma atroviride are two relevant fungi in agricultural systems. To gain insights into these organisms’ transcriptional gene regulatory networks (GRNs), we generated a manually curated transcription factor (TF) dataset for each of them, followed by a GRN inference utilizing available sequence motifs describing DNA-binding specificity and global gene expression data. As a proof of concept of the usefulness of this resource to pinpoint key transcriptional regulators, we employed publicly available transcriptomics data and a newly generated dual RNA-seq dataset to build context-specific Botrytis and Trichoderma GRNs under two different biological paradigms: exposure to continuous light and Botrytis-Trichoderma confrontation assays. Network analysis of fungal responses to constant light revealed striking differences in the transcriptional landscape of both fungi. On the other hand, we found that the confrontation of both microorganisms elicited a distinct set of differentially expressed genes with changes in T. atroviride exceeding those in B. cinerea. Using our regulatory network data, we were able to determine, in both fungi, central TFs involved in this interaction response, including TFs controlling a large set of extracellular peptidases in the biocontrol agent T. atroviride. In summary, our work provides a comprehensive catalog of transcription factors and regulatory interactions for both organisms. This catalog can now serve as a basis for generating novel hypotheses on transcriptional regulatory circuits in different experimental contexts.
format	article
author	Consuelo Olivares-Yañez Evelyn Sánchez Gabriel Pérez-Lara Aldo Seguel Pamela Y. Camejo Luis F. Larrondo Elena A. Vidal Paulo Canessa
author_facet	Consuelo Olivares-Yañez Evelyn Sánchez Gabriel Pérez-Lara Aldo Seguel Pamela Y. Camejo Luis F. Larrondo Elena A. Vidal Paulo Canessa
author_sort	Consuelo Olivares-Yañez
title	A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
title_short	A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
title_full	A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
title_fullStr	A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
title_full_unstemmed	A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
title_sort	comprehensive transcription factor and dna-binding motif resource for the construction of gene regulatory networks in botrytis cinerea and trichoderma atroviride
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/fdc93badae7e426db0522535e53543f1
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A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride

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