Universität zu Köln

Ignarski, Michael ORCID: 0000-0001-6057-7694, Rill, Constantin, Kaiser, Rainer W. J., Kaldirim, Madlen, Neuhaus, Rene, Esmaillie, Reza, Li, Xinping, Klein, Corinna, Bohl, Katrin, Petersen, Maike, Frese, Christian K., Hoehne, Martin, Atanassov, Ilian, Rinschen, Markus M., Hoepker, Katja, Schermer, Bernhard ORCID: 0000-0002-5194-9000, Benzing, Thomas, Dieterich, Christoph, Fabretti, Francesca and Mueller, Roman-Ulrich (2019). The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells. J. Am. Soc. Nephrol., 30 (4). S. 564 - 577. WASHINGTON: AMER SOC NEPHROLOGY. ISSN 1533-3450

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Abstract

Background RNA-binding proteins (RBPs) are fundamental regulators of cellular biology that affect all steps in the generation and processing of RNA molecules. Recent evidence suggests that regulation of RBPs that modulate both RNA stability and translation may have a profound effect on the proteome. However, regulation of RBPs in clinically relevant experimental conditions has not been studied systematically. Methods We used RNA interactome capture, a method for the global identification of RBPs to characterize the global RNA-binding proteome (RBPome) associated with polyA-tailed RNA species in murine ciliated epithelial cells of the inner medullary collecting duct. To study regulation of RBPs in a clinically relevant condition, we analyzed hypoxia-associated changes of the RBPome. Results We identified >1000 RBPs that had been previously found using other systems. In addition, we found a number of novel RBPs not identified by previous screens using mouse or human cells, suggesting that these proteins may be specific RBPs in differentiated kidney epithelial cells. We also found quantitative differences in RBP-binding to mRNA that were associated with hypoxia versus normoxia. Conclusions These findings demonstrate the regulation of RBPs through environmental stimuli and provide insight into the biology of hypoxia-response signaling in epithelial cells in the kidney. A repository of the RBPome and proteome in kidney tubular epithelial cells, derived from our findings, is freely accessible online, and may contribute to a better understanding of the role of RNA-protein interactions in kidney tubular epithelial cells, including the response of these cells to hypoxia.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Ignarski, Michael UNSPECIFIED orcid.org/0000-0001-6057-7694 UNSPECIFIED Rill, Constantin UNSPECIFIED UNSPECIFIED UNSPECIFIED Kaiser, Rainer W. J. UNSPECIFIED UNSPECIFIED UNSPECIFIED Kaldirim, Madlen UNSPECIFIED UNSPECIFIED UNSPECIFIED Neuhaus, Rene UNSPECIFIED UNSPECIFIED UNSPECIFIED Esmaillie, Reza UNSPECIFIED UNSPECIFIED UNSPECIFIED Li, Xinping UNSPECIFIED UNSPECIFIED UNSPECIFIED Klein, Corinna UNSPECIFIED UNSPECIFIED UNSPECIFIED Bohl, Katrin UNSPECIFIED UNSPECIFIED UNSPECIFIED Petersen, Maike UNSPECIFIED UNSPECIFIED UNSPECIFIED Frese, Christian K. UNSPECIFIED UNSPECIFIED UNSPECIFIED Hoehne, Martin UNSPECIFIED UNSPECIFIED UNSPECIFIED Atanassov, Ilian UNSPECIFIED UNSPECIFIED UNSPECIFIED Rinschen, Markus M. UNSPECIFIED UNSPECIFIED UNSPECIFIED Hoepker, Katja UNSPECIFIED UNSPECIFIED UNSPECIFIED Schermer, Bernhard UNSPECIFIED orcid.org/0000-0002-5194-9000 UNSPECIFIED Benzing, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Dieterich, Christoph UNSPECIFIED UNSPECIFIED UNSPECIFIED Fabretti, Francesca UNSPECIFIED UNSPECIFIED UNSPECIFIED Mueller, Roman-Ulrich UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-152027
DOI:	10.1681/ASN.2018090914
Journal or Publication Title:	J. Am. Soc. Nephrol.
Volume:	30
Number:	4
Page Range:	S. 564 - 577
Date:	2019
Publisher:	AMER SOC NEPHROLOGY
Place of Publication:	WASHINGTON
ISSN:	1533-3450
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language MESSENGER-RNA; WIDE IDENTIFICATION; BINDING PROTEINS; TARGET; GENES; HYDROCEPHALUS; OCCUPANCY; OXYGEN; SITES Multiple languages Urology & Nephrology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/15202