Single‐cell analysis of population context advances RNAi screening at multiple levels
Open Access
- 1 January 2012
- journal article
- research article
- Published by Springer Science and Business Media LLC in Molecular Systems Biology
- Vol. 8 (1), 579
- https://doi.org/10.1038/msb.2012.9
Abstract
Isogenic cells in culture show strong variability, which arises from dynamic adaptations to the microenvironment of individual cells. Here we study the influence of the cell population context, which determines a single cell's microenvironment, in image‐based RNAi screens. We developed a comprehensive computational approach that employs Bayesian and multivariate methods at the single‐cell level. We applied these methods to 45 RNA interference screens of various sizes, including 7 druggable genome and 2 genome‐wide screens, analysing 17 different mammalian virus infections and four related cell physiological processes. Analysing cell‐based screens at this depth reveals widespread RNAi‐induced changes in the population context of individual cells leading to indirect RNAi effects, as well as perturbations of cell‐to‐cell variability regulators. We find that accounting for indirect effects improves the consistency between siRNAs targeted against the same gene, and between replicate RNAi screens performed in different cell lines, in different labs, and with different siRNA libraries. In an era where large‐scale RNAi screens are increasingly performed to reach a systems‐level understanding of cellular processes, we show that this is often improved by analyses that account for and incorporate the single‐cell microenvironment.Keywords
This publication has 62 references indexed in Scilit:
- Origins of regulated cell-to-cell variabilityNature Reviews Molecular Cell Biology, 2011
- Non-genetic heterogeneity from stochastic partitioning at cell divisionNature Genetics, 2010
- Cell adhesion: integrating cytoskeletal dynamics and cellular tensionNature Reviews Molecular Cell Biology, 2010
- Functional genomic screen for modulators of ciliogenesis and cilium lengthNature, 2010
- Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genesNature, 2010
- The endocytic matrixNature, 2010
- Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivitiesMolecular Systems Biology, 2010
- What have RNAi screens taught us about viral–host interactions?Current Opinion in Microbiology, 2009
- Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noiseNature, 2006
- Expression profiling reveals off-target gene regulation by RNAiNature Biotechnology, 2003