RNA-binding proteins distinguish between similar sequence motifs to promote targeted deadenylation by Ccr4-Not
- MRC Laboratory of Molecular Biology, United Kingdom
Abstract
The Ccr4-Not complex removes mRNA poly(A) tails to regulate eukaryotic mRNA stability and translation. RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. Here, we reconstitute accelerated and selective deadenylation of RNAs containing AU-rich elements (AREs) and Pumilio-response elements (PREs). We find that the fission yeast homologues of Tristetraprolin/TTP and Pumilio/Puf (Zfs1 and Puf3) interact with Ccr4-Not via multiple regions within low-complexity sequences, suggestive of a multipartite interface that extends beyond previously defined interactions. Using a two-color assay to simultaneously monitor poly(A) tail removal from different RNAs, we demonstrate that Puf3 can distinguish between RNAs of very similar sequence. Analysis of binding kinetics reveals that this is primarily due to differences in dissociation rate constants. Consequently, motif quality is a major determinant of mRNA stability for Puf3 targets in vivo and can be used for the prediction of mRNA targets.
Data availability
All data generated during this study are included in the manuscript and supporting files. Source data are provided in Supplementary Files 1 and 2.
Article and author information
Author details
Funding
Medical Research Council (MC_U105192715)
- Lori A Passmore
Horizon 2020 Framework Programme (725685)
- Lori A Passmore
Seventh Framework Programme (261151)
- Lori A Passmore
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Rachel Green, Johns Hopkins School of Medicine, United States
Publication history
- Received: August 1, 2018
- Accepted: December 28, 2018
- Accepted Manuscript published: January 2, 2019 (version 1)
- Version of Record published: January 21, 2019 (version 2)
Copyright
© 2019, Webster et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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RNA-binding proteins distinguish between similar sequence motifs to promote targeted deadenylation by Ccr4-Not
eLife 8:e40670.
https://doi.org/10.7554/eLife.40670
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