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Target RNA motif and target mRNAs of the Quaking STAR protein

Nature Structural & Molecular Biology volume 12, pages 691–698 (2005)Cite this article

Abstract

Quaking viable (Qkv) mice have developmental defects that result in their characteristic tremor. The quaking (Qk) locus expresses alternatively spliced RNA-binding proteins belonging to the STAR family. To characterize the RNA binding specificity of the QKI proteins, we selected for RNA species that bound QKI from random pools of RNAs and defined the QKI response element (QRE) as a bipartite consensus sequence NACUAAY-N1–20-UAAY. A bioinformatic analysis using the QRE identified the three known RNA targets of QKI and 1,430 new putative mRNA targets, of which 23 were validated in vivo. A large proportion of the mRNAs are implicated in development and cell differentiation, as predicted from the phenotype of the Qkv mice. In addition, 24% are implicated in cell growth and/or maintenance, suggesting a role for QKI in cancer.

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Figure 1: Identification of QKI-specific RNA sequences using SELEX.
Figure 2: RNAs that bound to QKI-5 and their consensus sequence.
Figure 3: Defining the QRE.
Figure 4: Defining optimal distance and structure between direct repeats in the QRE.
Figure 5: Mapping QREs within two known mRNA targets of QKI, MBP and EGR-2.
Figure 6: Identification of new mRNA targets for Quaking.

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Acknowledgements

We thank M. Scott for the bioinformatic analyses and F. Major, P. Wilkinson and J. Côté for helpful discussions. This work was supported by grant MOP57692 from the Canadian Institutes of Health Research (CIHR) and by funds from the Multiple Sclerosis Society of Canada. A.G. is a Research Student of the National Cancer Institute of Canada supported with funds provided by the Terry Fox Run. S.R. is an Investigator of the CIHR.

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Authors and Affiliations

  1. Terry Fox Molecular Oncology Group and the Bloomfield Center for Research on Aging, and Departments of Oncology and Medicine, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, H3T 1E2, Québec, Canada

    André Galarneau & Stéphane Richard

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Correspondence to Stéphane Richard.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Comparison of the RNA binding affinity of QKI, QKI-6 and QKI-7 using a selected sequence. (PDF 125 kb)

Supplementary Fig. 2

QKI-5, QKI-6 and Sam68 specific immunoprecipitations. (PDF 157 kb)

Supplementary Table 1

mRNA targets identified based on the identified consensus. (PDF 107 kb)

Supplementary Table 2

Matrix based on the nucleotides identified by SELEX (PDF 103 kb)

Supplementary Table 3

mRNA targets identified based on the matrix (Supplementary Table 2) and a fixed core or half site sequence. (PDF 68 kb)

Supplementary Table 4

mRNA classification of each hit based on gene annotation. (PDF 10 kb)

Supplementary Table 5

Substrates used for all T7 RNA MegaShortscript. (PDF 32 kb)

Supplementary Table 6

Primers used for RT-PCR. (PDF 27 kb)

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Galarneau, A., Richard, S. Target RNA motif and target mRNAs of the Quaking STAR protein. Nat Struct Mol Biol 12, 691–698 (2005). https://doi.org/10.1038/nsmb963

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