Dual gene activation and knockout screen reveals directional dependencies in genetic networks.
Michael BoettcherRuilin TianJames A BlauEvan MarkegardRyan T WagnerDavid WuXiulei MoAnne BitonNoah ZaitlenHaian FuFrank McCormickMartin Edward KampmannMichael T McManusPublished in: Nature biotechnology (2018)
Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair. Based on the results from over 100,000 perturbed gene pairs, we reconstruct a directional dependency network for human K562 leukemia cells and demonstrate how our approach allows the determination of directionality in activating genetic interactions. Our interaction network connects previously uncharacterized genes to well-studied pathways and identifies targets relevant for therapeutic intervention.
Keyphrases
- genome wide
- copy number
- dna methylation
- genome wide identification
- staphylococcus aureus
- randomized controlled trial
- gene expression
- single cell
- induced apoptosis
- stem cells
- high resolution
- bone marrow
- cell death
- biofilm formation
- escherichia coli
- mass spectrometry
- pseudomonas aeruginosa
- transcription factor
- cell therapy
- genome editing
- network analysis