Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans

Summary: The cellular response to hypoxia is crucial to organismal survival, and hypoxia-inducible factors (HIF) are the key mediators of this response. HIF-signaling is central to many human diseases and mediates longevity in the nematode. Despite the rapidly increasing knowledge on RNA-binding pro...

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Main Authors:	Reza Esmaillie, Michael Ignarski, Katrin Bohl, Tim Krüger, Daniyal Ahmad, Lisa Seufert, Bernhard Schermer, Thomas Benzing, Roman-Ulrich Müller, Francesca Fabretti
Format:	Article
Language:	English
Published:	Elsevier 2019-12-01
Series:	iScience
Online Access:	http://www.sciencedirect.com/science/article/pii/S2589004219304900

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record_format	Article
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Reza Esmaillie Michael Ignarski Katrin Bohl Tim Krüger Daniyal Ahmad Lisa Seufert Bernhard Schermer Thomas Benzing Roman-Ulrich Müller Francesca Fabretti
spellingShingle	Reza Esmaillie Michael Ignarski Katrin Bohl Tim Krüger Daniyal Ahmad Lisa Seufert Bernhard Schermer Thomas Benzing Roman-Ulrich Müller Francesca Fabretti Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans iScience
author_facet	Reza Esmaillie Michael Ignarski Katrin Bohl Tim Krüger Daniyal Ahmad Lisa Seufert Bernhard Schermer Thomas Benzing Roman-Ulrich Müller Francesca Fabretti
author_sort	Reza Esmaillie
title	Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans
title_short	Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans
title_full	Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans
title_fullStr	Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans
title_full_unstemmed	Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans
title_sort	activation of hypoxia-inducible factor signaling modulates the rna protein interactome in caenorhabditis elegans
publisher	Elsevier
series	iScience
issn	2589-0042
publishDate	2019-12-01
description	Summary: The cellular response to hypoxia is crucial to organismal survival, and hypoxia-inducible factors (HIF) are the key mediators of this response. HIF-signaling is central to many human diseases and mediates longevity in the nematode. Despite the rapidly increasing knowledge on RNA-binding proteins (RBPs), little is known about their contribution to hypoxia-induced cellular adaptation. We used RNA interactome capture (RIC) in wild-type Caenorhabditis elegans and vhl-1 loss-of-function mutants to fill this gap. This approach identifies more than 1,300 nematode RBPs, 270 of which can be considered novel RBPs. Interestingly, loss of vhl-1 modulates the RBPome. This difference is not primarily explained by protein abundance suggesting differential RNA-binding. Taken together, our study provides a global view on the nematode RBPome and proteome as well as their modulation by HIF-signaling. The resulting RBP atlas is also provided as an interactive online data mining tool (http://shiny.cecad.uni-koeln.de:3838/celegans_rbpome). : Biological Sciences; Molecular Biology; Molecular Interaction; Molecular Network; Integrative Aspects of Cell Biology; Proteomics Subject Areas: Biological Sciences, Molecular Biology, Molecular Interaction, Molecular Network, Integrative Aspects of Cell Biology, Proteomics
url	http://www.sciencedirect.com/science/article/pii/S2589004219304900
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spelling	doaj-16cdefbfb256433681969347abc4e1a02020-11-25T01:15:34ZengElsevieriScience2589-00422019-12-0122466476Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegansReza Esmaillie0Michael Ignarski1Katrin Bohl2Tim Krüger3Daniyal Ahmad4Lisa Seufert5Bernhard Schermer6Thomas Benzing7Roman-Ulrich Müller8Francesca Fabretti9Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany; Systems Biology of Ageing Cologne, University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany; Systems Biology of Ageing Cologne, University of Cologne, Cologne 50931, GermanyDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany; Systems Biology of Ageing Cologne, University of Cologne, Cologne 50931, Germany; Corresponding authorDepartment II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne 50937, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne 50931, GermanySummary: The cellular response to hypoxia is crucial to organismal survival, and hypoxia-inducible factors (HIF) are the key mediators of this response. HIF-signaling is central to many human diseases and mediates longevity in the nematode. Despite the rapidly increasing knowledge on RNA-binding proteins (RBPs), little is known about their contribution to hypoxia-induced cellular adaptation. We used RNA interactome capture (RIC) in wild-type Caenorhabditis elegans and vhl-1 loss-of-function mutants to fill this gap. This approach identifies more than 1,300 nematode RBPs, 270 of which can be considered novel RBPs. Interestingly, loss of vhl-1 modulates the RBPome. This difference is not primarily explained by protein abundance suggesting differential RNA-binding. Taken together, our study provides a global view on the nematode RBPome and proteome as well as their modulation by HIF-signaling. The resulting RBP atlas is also provided as an interactive online data mining tool (http://shiny.cecad.uni-koeln.de:3838/celegans_rbpome). : Biological Sciences; Molecular Biology; Molecular Interaction; Molecular Network; Integrative Aspects of Cell Biology; Proteomics Subject Areas: Biological Sciences, Molecular Biology, Molecular Interaction, Molecular Network, Integrative Aspects of Cell Biology, Proteomicshttp://www.sciencedirect.com/science/article/pii/S2589004219304900

Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans

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