Abstract
In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. This did not occur when splicing was inhibited with U2 snRNA antisense morpholino oligonucleotide or the U2-snRNP-inactivating drug spliceostatin A unless U1 antisense morpholino oligonucleotide was also included. We further show that U1 snRNA–pre-mRNA base pairing was required to suppress premature cleavage and polyadenylation from nearby cryptic polyadenylation signals located in introns. These findings reveal a critical splicing-independent function for U1 snRNP in protecting the transcriptome, which we propose explains its overabundance.
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Acknowledgements
We are grateful to the members of our laboratory, especially J. Yong and J. Bachorik, for discussions and comments on this manuscript. We thank M. Yoshida for providing spliceostatin A. We also thank D. A. Baldwin and H. Rodriguez at the Microarray Core Facility at the University of Pennsylvania School of Medicine for help with the tiling array. This work was supported by the Association Française Contre les Myopathies (AFM). G.D. is an Investigator of the Howard Hughes Medical Institute.
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D.K., M.G.B., I.Y., M.K., L.N.S. and L.W. designed and performed experiments and contributed to data analysis. G.D. is responsible for the project planning and experimental design. All authors contributed to writing the paper.
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Kaida, D., Berg, M., Younis, I. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664–668 (2010). https://doi.org/10.1038/nature09479
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DOI: https://doi.org/10.1038/nature09479
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