Open AccessParallel reverse genetic screening in mutant human cells using transcriptomics
Author(s) -
Gapp Bianca V,
Konopka Tomasz,
Penz Thomas,
Dalal Vineet,
Bürckstümmer Tilmann,
Bock Christoph,
Nijman Sebastian MB
Publication year - 2016
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.15252/msb.20166890
Subject(s) - biology , mutant , transcriptome , computational biology , genetic screen , genetics , gene , gene expression
Reverse genetic screens have driven gene annotation and target discovery in model organisms. However, many disease‐relevant genotypes and phenotypes cannot be studied in lower organisms. It is therefore essential to overcome technical hurdles associated with large‐scale reverse genetics in human cells. Here, we establish a reverse genetic approach based on highly robust and sensitive multiplexed RNA sequencing of mutant human cells. We conduct 10 parallel screens using a collection of engineered haploid isogenic cell lines with knockouts covering tyrosine kinases and identify known and unexpected effects on signaling pathways. Our study provides proof of concept for a scalable approach to link genotype to phenotype in human cells, which has broad applications. In particular, it clears the way for systematic phenotyping of still poorly characterized human genes and for systematic study of uncharacterized genomic features associated with human disease.