Analysis and design of RNA sequencing experiments for identifying isoform regulation

Y Katz, ET Wang, EM Airoldi, CB Burge - Nature methods, 2010 - nature.com
Y Katz, ET Wang, EM Airoldi, CB Burge
Nature methods, 2010nature.com
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 …
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.
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