Abstract
The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFα mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ∼ 3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-κB pathway regulators such as IκBα and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with IκB kinase and NF-κB activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-κB pathway.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Binding Sites
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Blotting, Western
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DNA Damage
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DNA-Binding Proteins / metabolism*
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Electrophoresis, Polyacrylamide Gel
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Gene Expression Regulation
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Gene Knockdown Techniques
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HEK293 Cells
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Humans
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I-kappa B Proteins / metabolism*
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Intracellular Signaling Peptides and Proteins / metabolism*
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NF-KappaB Inhibitor alpha
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NF-kappa B / metabolism*
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Nuclear Proteins / metabolism*
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RNA Processing, Post-Transcriptional
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RNA Stability / genetics*
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RNA, Messenger / metabolism*
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RNA-Binding Proteins / genetics*
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Signal Transduction
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Tumor Necrosis Factor alpha-Induced Protein 3
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Ubiquitin-Protein Ligases / genetics*
Substances
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DNA-Binding Proteins
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I-kappa B Proteins
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Intracellular Signaling Peptides and Proteins
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NF-kappa B
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NFKBIA protein, human
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Nuclear Proteins
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RC3H1 protein, human
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RNA, Messenger
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RNA-Binding Proteins
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NF-KappaB Inhibitor alpha
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Ubiquitin-Protein Ligases
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TNFAIP3 protein, human
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Tumor Necrosis Factor alpha-Induced Protein 3