PgmNr W4129: Large-scale genetic interaction maps for C. elegans embryonic development.

Authors:
P. G. Cipriani 1,2 ; E. Munarriz 3 ; K. Erickson 1 ; J. Lucas 1,2 ; N. Smit 1 ; F. Ahmed 2 ; J. Reboul 4 ; K. Gunsalus 1,2 ; F. Piano 1,2


Institutes
1) New York University, New York, NY; 2) New York University Abu Dhabi, Abu Dhabi, UAE; 3) University of Buenos Aires, Buenos Aires, Argentina; 4) INSERM, France.


Keyword: Other ( genetic interaction )

Abstract:

Genetic interactions are functional associations between genes that are revealed upon simultaneous perturbation of two genetic loci. Genetic interactions provide information about how pathways buffer each other to maintain an organism’s homeostasis and can be used to identify previously unknown components and regulatory relationships within molecular networks. While only around 15% of genes appear to be essential on their own, expression studies tell us that over half of the transcriptome is typically expressed in any individual cell. To learn more about how essential and non-essential genes work together in embryonic development, we devised and implemented a high-throughput (HTP) system for RNAi-based genetic interaction studies. We first completed a pilot study testing a large set of predicted genetic interactions, and we have recently completed genome-wide enhancer and suppressor screens using 24 strains harboring temperature-sensitive alleles of genes that are essential for different aspects of early embryogenesis. The primary screen consisted of over 50 genome-wide RNAi screens in the conditional strains and over 30 additional screens in the N2 control, at multiple temperatures; we rescreened thousands of potential enhancers and suppressors in secondary assays with at least eight replicates. Suppressor interactions that were reproducible in multiple assays have been confirmed using both manual scoring and automated image analysis with our DevStaR algorithm (White et al., 2013). The final suppressor network links over 500 genes through more than 900 interactions; the enhancer network is not yet finalized, but based on results from our pilot study, we expect it to be much larger. We have archived all experimental results to enable quantitative scoring of embryonic lethality, and we have built a database for the millions of images collected with a web interface that allows querying and visualization of all the data collected in the screens. Analysis and follow-up studies of suppressor and enhancer interactions are ongoing.