Applying thiouracil tagging to mouse transcriptome analysis

Transcriptional profiling is a powerful approach to study mouse development, physiology, and disease models. Here, we describe a protocol for mouse thiouracil-tagging (TU-tagging), a transcriptome analysis technology that includes in vivo covalent labeling, purification, and analysis of cell type-specific RNA. TU-tagging enables 1) the isolation of RNA from a given cell population of a complex tissue, avoiding transcriptional changes induced by cell isolation trauma, and 2) the identification of actively transcribed RNAs and not pre-existing transcripts. Therefore, in contrast to other cell-specific transcriptional profiling methods based on purification of tagged ribosomes or nuclei, TU-tagging provides a direct examination of transcriptional regulation. We describe how to: 1) deliver 4-thiouracil to transgenic mice to thio-label cell lineage-specific transcripts, 2) purify TU-tagged RNA and prepare libraries for Illumina sequencing, and 3) follow a straight-forward bioinformatics workflow to identify cell type-enriched or differentially expressed genes. Tissue containing TU-tagged RNA can be obtained in one day, RNA-Seq libraries generated within two days, and, following sequencing, an initial bioinformatics analysis completed in one additional day.