TU-tagging: cell type–specific RNA isolation from intact complex tissues

We show that the combination of spatially restricted uracil phosphoribosyltransferase (UPRT) expression with 4-thiouracil (4TU) delivery can be used to label and purify cell type specific RNA from intact complex tissues in Drosophila melanogaster. This method is useful for isolating RNA from cell types that are difficult to isolate by dissection or dissociation methods and should work in many organisms, including mammals and other vertebrates. Cell type specific gene expression is a defining feature of multicellular organisms1. The analysis of cell type specific transcriptomes can provide insight into the mechanisms used to generate cellular diversity2, as well as help determine the underlying cause of disease3. Although a few methods are available for cell type specific RNA isolation4-7, each has constraints and researchers are often limited by their ability to isolate RNA from cell types of interest8. Thus, developing new methods for cell type specific RNA isolation is an important goal for genomic analysis of development and disease. We previously showed that the Toxoplasma gondii nucleotide salvage enzyme uracil phosphoribosyltransferase (UPRT) can be used to biosynthetically label newly synthesize