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

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dc.contributor.authorOlivares-Yanez, Consuelo
dc.contributor.authorSanchez, Evelyn
dc.contributor.authorPerez-Lara, Gabriel
dc.contributor.authorSeguel, Aldo
dc.contributor.authorCamejo, Pamela Y.
dc.contributor.authorLarrondo, Luis F.
dc.contributor.authorVidal, Elena A.
dc.contributor.authorCanessa, Paulo
dc.date.accessioned2025-01-20T22:03:43Z
dc.date.available2025-01-20T22:03:43Z
dc.date.issued2021
dc.description.abstractBotrytis 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. (C) 2021 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
dc.fuente.origenWOS
dc.identifier.doi10.1016/j.csbj.2021.11.012
dc.identifier.issn2001-0370
dc.identifier.urihttps://doi.org/10.1016/j.csbj.2021.11.012
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/94054
dc.identifier.wosidWOS:000731409400007
dc.language.isoen
dc.pagina.final6228
dc.pagina.inicio6212
dc.revistaComputational and structural biotechnology journal
dc.rightsacceso restringido
dc.subjectBotrytis cinerea
dc.subjectTrichoderma atroviride
dc.subjectTranscription factors
dc.subjectGene Regulatory Network
dc.subjectMycoparasitism
dc.titleA comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in <i>Botrytis cinerea</i> and <i>Trichoderma atroviride</i>
dc.typeartículo
dc.volumen19
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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