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Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

Abstract

The human and mouse genomes share a number of long, perfectly conserved nucleotide sequences, termed ultraconserved elements1. Whereas these regions can act as transcriptional enhancers when upstream of genes, those within genes are less well understood. In particular, the function of ultraconserved elements that overlap alternatively spliced exons of genes encoding RNA-binding proteins is unknown1,2. Here we report that in every member of the human SR family of splicing regulators, highly or ultraconserved elements are alternatively spliced, either as alternative ‘poison cassette exons’ containing early in-frame stop codons, or as alternative introns in the 3′ untranslated region. These alternative splicing events target the resulting messenger RNAs for degradation by means of an RNA surveillance pathway called nonsense-mediated mRNA decay. Mouse orthologues of the human SR proteins exhibit the same unproductive splicing patterns. Three SR proteins have been previously shown to direct splicing of their own transcripts, and one of these is known to autoregulate its expression by coupling alternative splicing with decay3,4,5; our results suggest that unproductive splicing is important for regulation of the entire SR family. We find that unproductive splicing associated with conserved regions has arisen independently in different SR genes, suggesting that splicing factors may readily acquire this form of regulation.

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Figure 1: SR gene alternative splice forms with PTCs are conserved between human and mouse and are associated with highly conserved and ultraconserved DNA elements.
Figure 2: SR gene alternative isoforms containing PTCs are degraded by NMD.

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Acknowledgements

We thank present and past members of the Brenner laboratory and J. Pleiss for discussions and comments on the manuscript, Q. Meng and D. Rio for expertise, A. Fisher for assistance, and the Feldman, Luan, Rio and Tjian laboratories for use of their equipment. This work was supported by NIH grants and a Sloan fellowship to S.E.B. L.F.L. was supported by an NIH training grant. R.E.G. is supported by an NSF postdoctoral fellowship in Biological Informatics.

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Correspondence to Steven E. Brenner.

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Competing Interests Statement: Our previous work in this area has resulted in three patent filings. US 7149631 ‘Alternative splicing and nonsense-mediated decay: computational methods and gene regulation’; application 10/637482 (pending) ‘RNA surveillance among curated proteins’; application 11/054155 (pending) ‘Nonsense suppressor agents in treatment of cutaneous and gastrointestinal disorders’. The first of these describes a computational method for identifying NMD-target isoforms and may cover the method used in this manuscript. The other patent filings discuss genes affected by alternative splicing and NMD, and therapeutic treatment. None of these patents mentions the specific results in this paper.

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Supplementary Information

This file contains Supplementary Methods and Results, Supplementary Figures S1-S5 with Legends, Supplementary Tables 1-5 and. additional references. (PDF 860 kb)

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Lareau, L., Inada, M., Green, R. et al. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446, 926–929 (2007). https://doi.org/10.1038/nature05676

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