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Nucleic Acids Research Advance Access originally published online on February 20, 2009
Nucleic Acids Research 2009 37(7):2227-2237; doi:10.1093/nar/gkp087
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Nucleic Acids Research, 2009, Vol. 37, No. 7 2227-2237
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures

You Li1, Eric S. Ho2, Samuel I. Gunderson2 and Megerditch Kiledjian1,*

1Department of Cell Biology and Neuroscience and 2Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854-8082, USA

*To whom correspondence should be addressed. Tel: +1 732 445 0796; Fax: +1 732 445 0104; Email: kiledjian{at}biology.rutgers.edu

Received December 8, 2008. Revised January 26, 2009. Accepted January 31, 2009.

mRNA decapping is a critical step in the control of mRNA stability and gene expression and is carried out by the Dcp2 protein. Dcp2 is an RNA-binding protein that must bind the RNA in order to recognize the cap for hydrolysis. We previously demonstrated that a 60 nucleotide (nt) element at the 5' end of the mRNA encoding Rrp41 is preferentially bound and decapped by Dcp2. Here, we demonstrate that enhanced decapping of this element is dependent on the structural integrity of its first 33 nt and not its primary sequence. The structure consists of a stem-loop positioned <10 nt from the 5' end of the mRNA. The generality of a stem-loop structure in enhanced Dcp2-mediated decapping was underscored by the identification of additional potential Dcp2 substrate mRNAs by a global analysis of human mRNAs containing a similar predicted stem-loop structure at their respective 5' end. These studies suggest a general role for 5' stem-loops in enhancing decapping activity and the utilization of this structure as a predictive tool for Dcp2 target substrates. These studies also demonstrate that Dcp2 alone in the absence of additional proteins can preferentially associate with and modulate mRNA decapping.


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