The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells

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.

A protein-RNA interaction atlas of the ribosome biogenesis factor AATF

“…Fig. 1A) 23 . In order to confirm this finding and to show it is not limited to our experiment we screened for the presence of AATF in published RIC datasets.…”

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

“…Proteins with an FDR lower than 0.05 for enrichment in crosslinked samples (student's ttest) are defined as class II RBPs. Proteins not reaching the criteria for either class I or class II in our study that had been identified as RBPs in previous RIC experiments are defined as “other RBPs” (Hentze et al., 2018, Ignarski et al., 2019, Queiroz et al., 2019, Tamburino et al., 2013, Trendel et al., 2019, Urdaneta et al., 2019). All remaining proteins are summarized under the term “no evidence.” We found that 45% of the proteins co-precipitated with RNA in WT and 38% of the proteins in the vhl-1 mutant fall into either class I or class II (Figure 2A, “RBPome” tab http://shiny.cecad.uni-koeln.de:3838/celegans_rbpome and Table S1).…”

“…To further characterize the C. elegans RBPome, we performed an in-depth comparison to published datasets from different model organisms summarized in a recent study (Hentze et al., 2018) and complemented it with an RBPome of murine cells cultured under hypoxia (Ignarski et al., 2019). More than half of class I and class II proteins identified in our study had previously been identified by RIC screens (Figure 2C).…”

“…As an example, this aspect was addressed regarding the induction of apoptosis in the only Caenorhabditis elegans ( C. elegans ) RIC dataset published to date (Matia-Gonzalez et al., 2015). In cell culture, a recent study from our group found differences in RBP-binding to RNA upon exposure to hypoxia (Ignarski et al., 2019). Key genes involved in sensing hypoxia are the hypoxia-inducible transcription factors (HIFs).…”

RNA Binding Motif 5 (RBM5) in the CNS—Moving Beyond Cancer to Harness RNA Splicing to Mitigate the Consequences of Brain Injury

“…A recent surge of disease-focused reviews have highlighted the emerging clinical interest for therapeutically targeting RBPs in the setting of: neurodegenerative diseases (Hofmann et al, 2019 ; Nussbacher et al, 2019 ), pain disorders (de la Pena and Campbell, 2018 ), cancer (Pereira et al, 2017 ), immunity (Turner and Díaz-Muñoz, 2018 ), diabetes (Nutter and Kuyumcu-Martinez, 2018 ), muscle wasting (Van Pelt et al, 2019 ), reproductive pathologies (Khalaj et al, 2017 ), cardiovascular disease (de Bruin et al, 2017 ), renal injury (Ignarski et al, 2019 ) and hepatic illness (Lee et al, 2020 ). Increased awareness of RBPs as targets has accelerated efforts to develop therapies that disrupt and/or modulate their activity.…”