A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits

Characterization of gene regulatory networks is fundamental to understanding homeostatic development. This process can be simplified by analyzing relatively simple genomes such as the genome of Drosophila melanogaster. In this work we have developed a computational framework in Drosophila to explore...

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Autores: Solorzano, Jacobo, Carrillo Santa de Pau, Enrique, Laguna, Teresa, Busturia, Ana
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/341717
Acceso en línea:http://hdl.handle.net/10261/341717
Access Level:acceso abierto
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spelling A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuitsSolorzano, JacoboCarrillo Santa de Pau, EnriqueLaguna, TeresaBusturia, AnaCharacterization of gene regulatory networks is fundamental to understanding homeostatic development. This process can be simplified by analyzing relatively simple genomes such as the genome of Drosophila melanogaster. In this work we have developed a computational framework in Drosophila to explore for the presence of gene regulatory circuits between two large groups of transcriptional regulators: the epigenetic group of the Polycomb/trithorax (PcG/trxG) proteins and the microRNAs (miRNAs). We have searched genome-wide for miRNA targets in PcG/trxG transcripts as well as for Polycomb Response Elements (PREs) in miRNA genes. Our results show that 10% of the analyzed miRNAs could be controlling PcG/trxG gene expression, while 40% of those miRNAs are putatively controlled by the selected set of PcG/trxG proteins. The integration of these analyses has resulted in the predicted existence of 3 classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits. In the first class, miRNA-PcG circuits are defined by miRNAs that reciprocally crosstalk with PcG. In the second, miRNA-trxG circuits are defined by miRNAs that reciprocally crosstalk with trxG. In the third class, miRNA-PcG/trxG shared circuits are defined by miRNAs that crosstalk with both PcG and trxG regulators. These putative regulatory circuits may uncover a novel mechanism in Drosophila for the control of PcG/trxG and miRNAs levels of expression. The computational framework developed here for Drosophila melanogaster can serve as a model case for similar analyses in other species. Moreover, our work provides, for the first time, a new and useful resource for the Drosophila community to consult prior to experimental studies investigating the epigenetic regulatory networks of miRNA-PcG/trxG mediated gene expression.This work was supported by PID2020-114533 ​GB-C21 grant from Spanish Agencia Estatal de Investigación/Ministerio de Ciencia e Innovación and by institutional grants from Fundación Areces and Banco Santander.Academic PressAgencia Estatal de Investigación (España)Ministerio de Ciencia e Innovación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2024202420232024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/341717reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114533GB-C21http://dx.doi.org/10.1016/j.ydbio.2022.12.008Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3417172026-05-22T06:33:51Z
dc.title.none.fl_str_mv A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
title A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
spellingShingle A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
Solorzano, Jacobo
title_short A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
title_full A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
title_fullStr A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
title_full_unstemmed A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
title_sort A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila: microRNA-Polycomb/trithorax circuits
dc.creator.none.fl_str_mv Solorzano, Jacobo
Carrillo Santa de Pau, Enrique
Laguna, Teresa
Busturia, Ana
author Solorzano, Jacobo
author_facet Solorzano, Jacobo
Carrillo Santa de Pau, Enrique
Laguna, Teresa
Busturia, Ana
author_role author
author2 Carrillo Santa de Pau, Enrique
Laguna, Teresa
Busturia, Ana
author2_role author
author
author
dc.contributor.none.fl_str_mv Agencia Estatal de Investigación (España)
Ministerio de Ciencia e Innovación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description Characterization of gene regulatory networks is fundamental to understanding homeostatic development. This process can be simplified by analyzing relatively simple genomes such as the genome of Drosophila melanogaster. In this work we have developed a computational framework in Drosophila to explore for the presence of gene regulatory circuits between two large groups of transcriptional regulators: the epigenetic group of the Polycomb/trithorax (PcG/trxG) proteins and the microRNAs (miRNAs). We have searched genome-wide for miRNA targets in PcG/trxG transcripts as well as for Polycomb Response Elements (PREs) in miRNA genes. Our results show that 10% of the analyzed miRNAs could be controlling PcG/trxG gene expression, while 40% of those miRNAs are putatively controlled by the selected set of PcG/trxG proteins. The integration of these analyses has resulted in the predicted existence of 3 classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits. In the first class, miRNA-PcG circuits are defined by miRNAs that reciprocally crosstalk with PcG. In the second, miRNA-trxG circuits are defined by miRNAs that reciprocally crosstalk with trxG. In the third class, miRNA-PcG/trxG shared circuits are defined by miRNAs that crosstalk with both PcG and trxG regulators. These putative regulatory circuits may uncover a novel mechanism in Drosophila for the control of PcG/trxG and miRNAs levels of expression. The computational framework developed here for Drosophila melanogaster can serve as a model case for similar analyses in other species. Moreover, our work provides, for the first time, a new and useful resource for the Drosophila community to consult prior to experimental studies investigating the epigenetic regulatory networks of miRNA-PcG/trxG mediated gene expression.
publishDate 2023
dc.date.none.fl_str_mv 2023
2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/341717
url http://hdl.handle.net/10261/341717
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114533GB-C21
http://dx.doi.org/10.1016/j.ydbio.2022.12.008
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Academic Press
publisher.none.fl_str_mv Academic Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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