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Nucleic Acids Research Advance Access originally published online on August 6, 2008
Nucleic Acids Research 2008 36(16):5290-5296; doi:10.1093/nar/gkn509
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Nucleic Acids Research, 2008, Vol. 36, No. 16 5290-5296
© 2008 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

The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets

María Flor García-Mayoral, Irene Díaz-Moreno, David Hollingworth and Andres Ramos*

MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK

*To whom correspondence should be addressed. Tel: 44 020 88162550; Fax: 44 020 89064477; Email: aramos{at}nimr.mrc.ac.uk

Received May 20, 2008. Revised July 23, 2008. Accepted July 24, 2008.

K-homology (KH) splicing regulator protein (KSRP) is a multi-domain RNA-binding protein that regulates different steps of mRNA metabolism, from mRNA splicing to mRNA decay, interacting with a broad range of RNA sequences. To understand how KSRP recognizes its different RNA targets it is necessary to define the general rules of KSRP–RNA interaction. We describe here a complete scaffold-independent analysis of the RNA-binding potential of the four KH domains of KSRP. The analysis shows that KH3 binds to the RNA with a significantly higher affinity than the other domains and recognizes specifically a G-rich target. It also demonstrates that the other KH domains of KSRP display different sequence preferences explaining the broad range of targets recognized by the protein. Further, KSRP shows a strong negative selectivity for sequences containing several adjacent Cytosines limiting the target choice of KSRP within single-stranded RNA regions. The in-depth analysis of the RNA-binding potential of the KH domains of KSRP provides us with an understanding of the role of low sequence specificity domains in RNA recognition by multi-domain RNA-binding proteins.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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