Analysis and design of RNA sequencing experiments for identifying isoform regulation
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Burge_Analysis and design.pdf
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Author(s)
Katz, Yarden
Airoldi, Edoardo M.
Wang, Eric T
Burge, Christopher B
Date Issued
November 2010
Journal
Nature Methods
Publisher
Nature Publishing Group
Citation
Katz, Yarden, Eric T Wang, Edoardo M Airoldi, and Christopher B Burge. “Analysis and design of RNA sequencing experiments for identifying isoform regulation.” Nature Methods 7, no. 12 (November 7, 2010): 1009-1015.
Version
Author's final manuscript
Abstract
Through alternative splicing, most human genes express multiple isoforms that often differ in function. To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced exons and isoforms and assesses confidence in these estimates. Incorporation of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of alternative-splicing levels. MISO also detects differentially regulated exons or isoforms. Application of MISO implicated the RNA splicing factor hnRNP H1 in the regulation of alternative cleavage and polyadenylation, a role that was supported by UV cross-linking–immunoprecipitation sequencing (CLIP-seq) analysis in human cells. Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre-mRNA processing and yield guidelines for the optimal design of RNA-seq experiments for studies of gene and isoform expression.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Biology
Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1038/nmeth.1528
