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Nucleic Acids Res. 2008 Sep;36(16):5290-6. doi: 10.1093/nar/gkn509. Epub 2008 Aug 6.

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

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

Abstract

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.

PMID:
18684992
[PubMed - indexed for MEDLINE]
PMCID:
PMC2532734
Free PMC Article

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