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| Status |
Public on Feb 29, 2020 |
| Title |
Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Systematic mapping of genetic interactions and interrogation of the functions of sizeable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR-based screening system for combinatorial genetic manipulation that employs co-expression of Cas9 and Cas12a nucleases and machine learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named CHyMErA (Cas Hybrid for Multiplexed Editing and Screening Applications), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive genetic interactions and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemo-genetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for genetic interaction mapping and the functional analysis of sizeable genomic regions, such as alternative exons.
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| Overall design |
RNA-Seq of HAP1N2A cells upon RNAi-mediated knockdown RBM26, RBM27, bothf11, or control non-targeting knockdown, in two replicates.
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| Contributor(s) |
Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KC, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J |
| Citation(s) |
32249828 |
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| Submission date |
Jan 22, 2020 |
| Last update date |
Apr 28, 2020 |
| Contact name |
Ulrich Braunschweig |
| Organization name |
University of Toronto
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| Department |
Donnelly Centre
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| Lab |
Benjamin J. Blencowe
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| Street address |
160 College Street
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S 3E1 |
| Country |
Canada |
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| Platforms (1) |
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| Samples (8)
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| GSM4279264 |
siNT.A: RNA-Seq of HAP1 cells after control non-targeting knockdown, replicate 1 |
| GSM4279265 |
siRBM26.A: RNA-Seq of HAP1 cells after knockdown of RBM26, replicate 1 |
| GSM4279266 |
siRBM27.A: RNA-Seq of HAP1 cells after knockdown of RBM27, replicate 1 |
| GSM4279267 |
siRBM26.27.A: RNA-Seq of HAP1 cells after double knockdown of RBM26 and RBM27, replicate 1 |
| GSM4279268 |
siNT.B: RNA-Seq of HAP1 cells after control non-targeting knockdown, replicate 2 |
| GSM4279269 |
siRBM26.B: RNA-Seq of HAP1 cells after knockdown of RBM26, replicate 2 |
| GSM4279270 |
siRBM27.B: RNA-Seq of HAP1 cells after knockdown of RBM27, replicate 2 |
| GSM4279271 |
siRBM26.27.B: RNA-Seq of HAP1 cells after double knockdown of RBM26 and RBM27, replicate 2 |
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| Relations |
| BioProject |
PRJNA602699 |
| SRA |
SRP243927 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144078_DE.tab.gz |
1.3 Mb |
(ftp)(http) |
TAB |
| GSE144078_RBM26.27_transcReadCounts.tab.gz |
11.2 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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