U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

By D. Kaida, Michael G. Berg, Ihab Younis, M. Kasim, Larry N. Singh, L. Wan, G. Dreyfuss. Nature, 2010

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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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2bdaf81a1f298ab3937468f9eb8f223918102439

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Citations in the corpus

The nuts and bolts of the endogenous spliceosome (2017, methodology): “Yet, only U1 snRNP was found at the transcription site of the intronless gene E1, suggesting that only U1 snRNP is associated with intronless transcripts, consistent with U1 snRNP additional role in 30end processing.(43) Association of U1 snRNP alone with intronless transcripts needs further testing”
circRNA biogenesis competes with pre-mRNA splicing. (2014, background): “Although well coordinated, RNA-processing events can compete with each other as in alternative splicing, cleavage, and polyadenylation in intronic regions (Kaida et al., 2010; Zhao and Manley, 1996) and synthesis of pre-miRNAs located at intron-exon junctions (Melamed et al.”
Systematic discovery of Xist RNA binding proteins (2015, background): “U1 selectively enriched for the CSTF complex involved in pre-mRNA cleavage and polyadenylation, a recently described non-canonical function of U1 (Figures 2C and S2B; Gene Ontology (GO) term ‘‘RNA 30-end processing’’ in Figure S1A) (Berg et al., 2012; Kaida et al., 2010).”
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, positive): “Furthermore, PASs are depleted and U1 snRNP recognition sites (SS5s) are enriched in the sense direction, consistent with observations that the U1 snRNP complex protects pre-mRNAs from cleavage and polyadenylation 50, 51 .”
Ending the message: poly(A) signals then and now. (2011, background): “These viral examples of PAS regulation by 59SS repression have now been generalized to the whole genome by a recent study that tested the effect of blocking U1snRNA by antisense RNA analogs (morpholino) that were electroporated into mammalian cells (Kaida et al. 2010).”