Integration profiling of gene function with dense maps of transposon integration

Yabin Guo, Jung Min Park, Bowen Cui, Elizabeth Humes, Sunil Gangadharan, Stevephen Hung, Peter C. FitzGerald, Kwang Lae Hoe, Shiv I.S. Grewal, Nancy L. Craig, Henry L. Levin

Research output: Contribution to journalArticlepeer-review

Abstract

Understanding how complex networks of genes integrate to produce dividing cells is an important goal that is limited by the difficulty in defining the function of individual genes. Current resources for the systematic identification of gene function such as siRNA libraries and collections of deletion strains are costly and organism specific. We describe here integration profiling, a novel approach to identify the function of eukaryotic genes based upon dense maps of transposon integration. As a proof of concept, we used the transposon Hermes to generate a library of 360,513 insertions in the genome of Schizosaccharomyces pombe. On average, we obtained one insertion for every 29 bp of the genome. Hermes integrated more often into nucleosome free sites and 33% of the insertions occurred in ORFs. We found that ORFs with low integration densities successfully identified the genes that are essential for cell division. Importantly, the nonessential ORFs with intermediate levels of insertion correlated with the nonessential genes that have functions required for colonies to reach full size. This finding indicates that integration profiles can measure the contribution of nonessential genes to cell division. While integration profiling succeeded in identifying genes necessary for propagation, it also has the potential to identify genes important for many other functions such as DNA repair, stress response, and meiosis.

Original languageEnglish (US)
Pages (from-to)599-609
Number of pages11
JournalGenetics
Volume195
Issue number2
DOIs
StatePublished - Oct 2013

ASJC Scopus subject areas

  • Genetics

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