Characterization of RNA-binding proteins possibly involved in modulating human AT1 receptor mRNA stability

AbstractFollowing the realization that eukaryotic RNA-binding proteomes are substantially larger than anticipated, we must now understand their detailed composition and dynamics. Methods such as RNA interactome capture (RIC) have begun to address this need. However, limitations of RIC have been reported. Here we describe enhanced RNA interactome capture (eRIC), a method based on the use of an LNA-modified capture probe, which yields numerous advantages including greater specificity and increased signal-to-noise ratios compared to existing methods. In Jurkat cells, eRIC reduces the rRNA and DNA contamination by >10-fold compared to RIC and increases the detection of RNA-binding proteins. Due to its low background, eRIC also empowers comparative analyses of changes of RNA-bound proteomes missed by RIC. For example, in cells treated with dimethyloxalylglycine, which inhibits RNA demethylases, eRIC identifies m6A-responsive RNA-binding proteins that escape RIC. eRIC will facilitate the unbiased characterization of RBP dynamics in response to biological and pharmacological cues.

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Characterization of glycine-rich RNA-binding proteins inBrassica napusunder stress conditions

Physiologia Plantarum ◽

10.1111/j.1399-3054.2012.01628.x ◽

2012 ◽

Vol 146 (3) ◽

pp. 297-307 ◽

Cited By ~ 12

Author(s):

Min Kyung Kim ◽

Hyun Ju Jung ◽

Dong Hyun Kim ◽

Hunseung Kang

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Stress Conditions

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Control of Cytokine mRNA Expression by RNA-binding Proteins and microRNAs

Journal of Dental Research ◽

10.1177/0022034512437372 ◽

2012 ◽

Vol 91 (7) ◽

pp. 651-658 ◽

Cited By ~ 60

Author(s):

V. Palanisamy ◽

A. Jakymiw ◽

E.A. Van Tubergen ◽

N.J. D’Silva ◽

K.L. Kirkwood

Keyword(s):

Cancer Progression ◽

Mrna Stability ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Periodontal Diseases ◽

Pharyngeal Cancer ◽

Cytokine Mrna ◽

Mediators Of Inflammation ◽

The Stability

Cytokines are critical mediators of inflammation and host defenses. Regulation of cytokines can occur at various stages of gene expression, including transcription, mRNA export, and post- transcriptional and translational levels. Among these modes of regulation, post-transcriptional regulation has been shown to play a vital role in controlling the expression of cytokines by modulating mRNA stability. The stability of cytokine mRNAs, including TNFα, IL-6, and IL-8, has been reported to be altered by the presence of AU-rich elements (AREs) located in the 3′-untranslated regions (3′UTRs) of the mRNAs. Numerous RNA-binding proteins and microRNAs bind to these 3′UTRs to regulate the stability and/or translation of the mRNAs. Thus, this paper describes the cooperative function between RNA-binding proteins and miRNAs and how they regulate AU-rich elements containing cytokine mRNA stability/degradation and translation. These mRNA control mechanisms can potentially influence inflammation as it relates to oral biology, including periodontal diseases and oral pharyngeal cancer progression.

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Identification and Characterization of RNA-binding Proteins through Three-hybrid Analysis

Handbook of RNA Biochemistry ◽

10.1002/9783527619504.ch45 ◽

2008 ◽

pp. 737-754

Author(s):

Felicia Scott ◽

David R. Engelke

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Hybrid Analysis ◽

Identification And Characterization

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An Interaction between Two RNA Binding Proteins, Nab2 and Pub1, Links mRNA Processing/Export and mRNA Stability

Molecular and Cellular Biology ◽

10.1128/mcb.00881-07 ◽

2007 ◽

Vol 27 (18) ◽

pp. 6569-6579 ◽

Cited By ~ 16

Author(s):

Luciano H. Apponi ◽

Seth M. Kelly ◽

Michelle T. Harreman ◽

Alexander N. Lehner ◽

Anita H. Corbett ◽

...

Keyword(s):

Mrna Stability ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Protein ◽

Tail Length ◽

Functional Link ◽

Mrna Binding Protein ◽

Mrna Binding

ABSTRACT mRNA stability is modulated by elements in the mRNA transcript and their cognate RNA binding proteins. Poly(U) binding protein 1 (Pub1) is a cytoplasmic Saccharomyces cerevisiae mRNA binding protein that stabilizes transcripts containing AU-rich elements (AREs) or stabilizer elements (STEs). In a yeast two-hybrid screen, we identified nuclear poly(A) binding protein 2 (Nab2) as being a Pub1-interacting protein. Nab2 is an essential nucleocytoplasmic shuttling mRNA binding protein that regulates poly(A) tail length and mRNA export. The interaction between Pub1 and Nab2 was confirmed by copurification and in vitro binding assays. The interaction is mediated by the Nab2 zinc finger domain. Analysis of the functional link between these proteins reveals that Nab2, like Pub1, can modulate the stability of specific mRNA transcripts. The half-life of the RPS16B transcript, an ARE-like sequence-containing Pub1 target, is decreased in both nab2-1 and nab2-67 mutants. In contrast, GCN4, an STE-containing Pub1 target, is not affected. Similar results were obtained for other ARE- and STE-containing Pub1 target transcripts. Further analysis reveals that the ARE-like sequence is necessary for Nab2-mediated transcript stabilization. These results suggest that Nab2 functions together with Pub1 to modulate mRNA stability and strengthen a model where nuclear events are coupled to the control of mRNA turnover in the cytoplasm.

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