Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
- Arshad H. Khan1,
- Andy Lin2,
- Richard T. Wang3,
- Joshua S. Bloom3,4,
- Kenneth Lange3 and
- Desmond J. Smith1
- 1Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1735, USA;
- 2Office of Information Technology, UCLA, Los Angeles, California 90095-1557, USA;
- 3Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA;
- 4Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA
Abstract
Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci, and three loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene. Divergent properties were displayed by the RH-BSA growth genes compared to those from loss-of-function screens, refuting the balance hypothesis. In addition, enhanced retention of human centromeres in the RH pools suggests a new approach to functional dissection of these chromosomal elements. Pooled analysis of RH cells showed high power and resolution and should be a useful addition to the mammalian genetic toolkit.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.262204.120.
- Received February 10, 2020.
- Accepted August 26, 2020.
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