Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling
RNA Therapeutics Institute; Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology; Program in Systems Biology
Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology
Full understanding of eukaryotic transcriptomes and how they respond to different conditions requires deep knowledge of all sites of intron excision. Although RNA sequencing (RNA-seq) provides much of this information, the low abundance of many spliced transcripts (often due to their rapid cytoplasmic decay) limits the ability of RNA-seq alone to reveal the full repertoire of spliced species. Here, we present "spliceosome profiling," a strategy based on deep sequencing of RNAs co-purifying with late-stage spliceosomes. Spliceosome profiling allows for unambiguous mapping of intron ends to single-nucleotide resolution and branchpoint identification at unprecedented depths. Our data reveal hundreds of new introns in S. pombe and numerous others that were previously misannotated. By providing a means to directly interrogate sites of spliceosome assembly and catalysis genome-wide, spliceosome profiling promises to transform our understanding of RNA processing in the nucleus, much as ribosome profiling has transformed our understanding mRNA translation in the cytoplasm.
DOI of Published Version
Cell. 2018 May 3;173(4):1031-1044.e13. doi: 10.1016/j.cell.2018.03.062. Link to article on publisher's site
Chen W, Moore JE, Ozadam H, Shulha HP, Rhind N, Weng Z, Moore MJ. (2018). Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling. Program in Bioinformatics and Integrative Biology Publications. https://doi.org/10.1016/j.cell.2018.03.062. Retrieved from https://escholarship.umassmed.edu/bioinformatics_pubs/127