U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

Nature. 2010 Dec 2;468(7324):664-8. doi: 10.1038/nature09479. Epub 2010 Sep 29.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • HeLa Cells
  • Humans
  • Introns / genetics
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Oligonucleotides, Antisense / genetics
  • Oligonucleotides, Antisense / metabolism
  • Oligonucleotides, Antisense / pharmacology
  • Polyadenylation* / drug effects
  • Polyadenylation* / genetics
  • Pyrans / pharmacology
  • RNA Precursors / genetics
  • RNA Precursors / metabolism*
  • RNA Splicing* / drug effects
  • RNA Splicing* / genetics
  • RNA, Small Nuclear / genetics
  • RNA, Small Nuclear / metabolism
  • Ribonucleoprotein, U1 Small Nuclear / antagonists & inhibitors
  • Ribonucleoprotein, U1 Small Nuclear / genetics
  • Ribonucleoprotein, U1 Small Nuclear / metabolism*
  • Spiro Compounds / pharmacology


  • Oligonucleotides, Antisense
  • Pyrans
  • RNA Precursors
  • RNA, Small Nuclear
  • Ribonucleoprotein, U1 Small Nuclear
  • Spiro Compounds
  • U1 small nuclear RNA
  • U2 small nuclear RNA
  • spliceostatin A

Associated data

  • GEO/GSE24179