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RNA secondary structure in mutually exclusive splicing

Abstract

Mutually exclusive splicing is a regulated means to generate protein diversity, but the underlying mechanisms are poorly understood. Here comparative genome analysis revealed the built-in intronic elements for controlling mutually exclusive splicing of the 14-3-3ξ pre-mRNA. These elements are clade specific but are evolutionarily conserved at the secondary structure level. Combined evidence revealed the triple functions of these inter-intronic RNA pairings in synergistically ensuring the selection of only one of multiple exons, through activation of the proximal variable exon outside the loop by the approximation of cis elements, and simultaneous repression of the exon within the loop, in combination with the physical competition of RNA pairing. Additionally, under this model, we also deciphered a similar structural code in exon clusters 4 and 9 of Dscam (38,016 isoforms) and Mhc (480 isoforms). Our findings suggest a broadly applicable mechanism to ensure mutually exclusive splicing.

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Figure 1: Phylogenetic arrangement of cis intronic elements in insect 14-3-3ξ genes.
Figure 2: Mutually exclusive splicing is directed by competing RNA secondary structures.
Figure 3: RNA pairing controls the switching of mutually exclusive exons in B. mori 14-3-3ξ pre-mRNA.
Figure 4: Mutually exclusive splicing is regulated by base-pairing strength and inter-distance.
Figure 5: The effect of the distance between the 5′ splice site and the selectors on the efficiency of exon selection.
Figure 6: RNA pairing interaction functions to approximate upstream and downstream sequences.
Figure 7: Similar structural codes within the exon clusters 4 and 9 of Dscam and Mhc gene.
Figure 8: Models for the control and regulation of mutually exclusive splicing.

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Acknowledgements

This work was partly supported by research grants from the National Natural Science Foundation of China (90508007, 30770469), the Natural Science Foundation of Zhejiang Province (no. R3090177), the 863 Program (2006AA10A119), the National Science and Technology Project (2009ZX09103-694) and the Program for New Century Excellent Talents in University (NCET-04-0531).

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Authors and Affiliations

Authors

Contributions

Y.Y., W.Z., L.Z. and W.W. conducted mutational studies and splicing analyses; L.Z. collected, cloned and analyzed the nucleotide sequences; W.Z. was responsible for tissue-specific analyses of mutually exclusive splicing; F.S. conducted mutational studies and splicing analyses in silkworm; H.W., D.S. and Y. Jiang made the DNA constructs; N.T. and J.B. analyzed sequence data and RNA secondary structures. Y. Jin conceived of this project, designed the experiments, analyzed the data and wrote the manuscript; Y.Z. analyzed the data; all authors discussed the results and commented on the manuscript.

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Correspondence to Yongfeng Jin.

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The authors declare no competing financial interests.

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Supplementary Figures 1–7, Supplementary Tables 1–2 and Supplementary Results (PDF 946 kb)

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Yang, Y., Zhan, L., Zhang, W. et al. RNA secondary structure in mutually exclusive splicing. Nat Struct Mol Biol 18, 159–168 (2011). https://doi.org/10.1038/nsmb.1959

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