A gene toolbox for monitoring autophagy transcription

Abstract Autophagy is a highly dynamic and multi-step process, regulated by many functional protein units. Here, we have built up a comprehensive and up-to-date annotated gene list for the autophagy pathway, by combining previously published gene lists and the most recent publications in the field....

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Autores principales:	Matteo Bordi, Rossella De Cegli, Beatrice Testa, Ralph A. Nixon, Andrea Ballabio, Francesco Cecconi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Publishing Group 2021
Materias:	Cytology QH573-671
Acceso en línea:	https://doaj.org/article/338415c43c534bd48426adcb5bf1eff0
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id	oai:doaj.org-article:338415c43c534bd48426adcb5bf1eff0
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spelling	oai:doaj.org-article:338415c43c534bd48426adcb5bf1eff02021-11-07T12:05:23ZA gene toolbox for monitoring autophagy transcription10.1038/s41419-021-04121-92041-4889https://doaj.org/article/338415c43c534bd48426adcb5bf1eff02021-11-01T00:00:00Zhttps://doi.org/10.1038/s41419-021-04121-9https://doaj.org/toc/2041-4889Abstract Autophagy is a highly dynamic and multi-step process, regulated by many functional protein units. Here, we have built up a comprehensive and up-to-date annotated gene list for the autophagy pathway, by combining previously published gene lists and the most recent publications in the field. We identified 604 genes and created main categories: MTOR and upstream pathways, autophagy core, autophagy transcription factors, mitophagy, docking and fusion, lysosome and lysosome-related genes. We then classified such genes in sub-groups, based on their functions or on their sub-cellular localization. Moreover, we have curated two shorter sub-lists to predict the extent of autophagy activation and/or lysosomal biogenesis; we next validated the “induction list” by Real-time PCR in cell lines during fasting or MTOR inhibition, identifying ATG14, ATG7, NBR1, ULK1, ULK2, and WDR45, as minimal transcriptional targets. We also demonstrated that our list of autophagy genes can be particularly useful during an effective RNA-sequencing analysis. Thus, we propose our lists as a useful toolbox for performing an informative and functionally-prognostic gene scan of autophagy steps.Matteo BordiRossella De CegliBeatrice TestaRalph A. NixonAndrea BallabioFrancesco CecconiNature Publishing GrouparticleCytologyQH573-671ENCell Death and Disease, Vol 12, Iss 11, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Cytology QH573-671
spellingShingle	Cytology QH573-671 Matteo Bordi Rossella De Cegli Beatrice Testa Ralph A. Nixon Andrea Ballabio Francesco Cecconi A gene toolbox for monitoring autophagy transcription
description	Abstract Autophagy is a highly dynamic and multi-step process, regulated by many functional protein units. Here, we have built up a comprehensive and up-to-date annotated gene list for the autophagy pathway, by combining previously published gene lists and the most recent publications in the field. We identified 604 genes and created main categories: MTOR and upstream pathways, autophagy core, autophagy transcription factors, mitophagy, docking and fusion, lysosome and lysosome-related genes. We then classified such genes in sub-groups, based on their functions or on their sub-cellular localization. Moreover, we have curated two shorter sub-lists to predict the extent of autophagy activation and/or lysosomal biogenesis; we next validated the “induction list” by Real-time PCR in cell lines during fasting or MTOR inhibition, identifying ATG14, ATG7, NBR1, ULK1, ULK2, and WDR45, as minimal transcriptional targets. We also demonstrated that our list of autophagy genes can be particularly useful during an effective RNA-sequencing analysis. Thus, we propose our lists as a useful toolbox for performing an informative and functionally-prognostic gene scan of autophagy steps.
format	article
author	Matteo Bordi Rossella De Cegli Beatrice Testa Ralph A. Nixon Andrea Ballabio Francesco Cecconi
author_facet	Matteo Bordi Rossella De Cegli Beatrice Testa Ralph A. Nixon Andrea Ballabio Francesco Cecconi
author_sort	Matteo Bordi
title	A gene toolbox for monitoring autophagy transcription
title_short	A gene toolbox for monitoring autophagy transcription
title_full	A gene toolbox for monitoring autophagy transcription
title_fullStr	A gene toolbox for monitoring autophagy transcription
title_full_unstemmed	A gene toolbox for monitoring autophagy transcription
title_sort	gene toolbox for monitoring autophagy transcription
publisher	Nature Publishing Group
publishDate	2021
url	https://doaj.org/article/338415c43c534bd48426adcb5bf1eff0
work_keys_str_mv	AT matteobordi agenetoolboxformonitoringautophagytranscription AT rosselladecegli agenetoolboxformonitoringautophagytranscription AT beatricetesta agenetoolboxformonitoringautophagytranscription AT ralphanixon agenetoolboxformonitoringautophagytranscription AT andreaballabio agenetoolboxformonitoringautophagytranscription AT francescocecconi agenetoolboxformonitoringautophagytranscription AT matteobordi genetoolboxformonitoringautophagytranscription AT rosselladecegli genetoolboxformonitoringautophagytranscription AT beatricetesta genetoolboxformonitoringautophagytranscription AT ralphanixon genetoolboxformonitoringautophagytranscription AT andreaballabio genetoolboxformonitoringautophagytranscription AT francescocecconi genetoolboxformonitoringautophagytranscription
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A gene toolbox for monitoring autophagy transcription

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