Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution

Jordan E. Burke, Adam D. Longhurst, Daria Merkurjev, Jade Sales-Lee, Beiduo Rao, James J. Moresco, John R. Yates, Jingyi Jessica Li, Hiten D. Madhani

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Tools to understand how the spliceosome functions in vivo have lagged behind advances in the structural biology of the spliceosome. Here, methods are described to globally profile spliceosome-bound pre-mRNA, intermediates, and spliced mRNA at nucleotide resolution. These tools are applied to three yeast species that span 600 million years of evolution. The sensitivity of the approach enables the detection of canonical and non-canonical events, including interrupted, recursive, and nested splicing. This application of statistical modeling uncovers independent roles for the size and position of the intron and the number of introns per transcript in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal the ATP-dependent discard of numerous endogenous substrates after spliceosome assembly in vivo and connect this discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology used to investigate an RNP central to eukaryotic gene expression. Quantitative in vivo spliceosome profiling in three divergent yeast species reveals unannotated splicing events and determinants of catalytic efficiency and assesses non-optimal substrates.

Original languageEnglish (US)
Pages (from-to)1014-1030.e17
JournalCell
Volume173
Issue number4
DOIs
Publication statusPublished - May 3 2018
Externally publishedYes

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Keywords

  • pre-mRNA splicing
  • spliceosome
  • splicing catalysis
  • splicing fidelity

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Burke, J. E., Longhurst, A. D., Merkurjev, D., Sales-Lee, J., Rao, B., Moresco, J. J., ... Madhani, H. D. (2018). Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution. Cell, 173(4), 1014-1030.e17. https://doi.org/10.1016/j.cell.2018.03.020