BEAM: a combinatorial recombinase toolbox for binary gene expression and mosaic genetic analysis
We describe a system for mosaic genetic analysis termed BEAM, which relies on exogenous DNA delivery in combination with sparse recombinase activation to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Following transfection or viral transduction, combinatorial recombinase activity generates two distinct populations of cells labeled with either green or red fluorescent protein. BEAM relies on recombinase-dependent signal amplification and delayed reporter expression to enable sharper delineation of control and experimental cells, and to improve reliability of relative to existing methods. We applied BEAM to a variety of known phenotypes to illustrate its advantages for identifying temporally or spatially aberrant phenotypes, for revealing changes in cell proliferation or death, and for controlling for procedural variability. In addition, we used BEAM to test the cortical protomap hypothesis at the individual radial unit level, revealing that area identity is cell-autonomously specified in adjacent radial units. Overall design: BEAM plasmids were electroporated into the developing cerebral cortex of Couptf1-fl/fl mice at E14.5 and somatosensory cortex was collected at P3. The tissue was dissociated and RFP- and GFP-labeled cells were FACS purified. We then performed RNAseq gene expression analysis, and identified differentially expressed transcripts