GSE123421
Tagger–a Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice [TU-Tag-RNA-seq]
We developed a knock-in mouse line that combines four enrichment tools to study gene regulatory networks of the brain and other complex tissues. As a result, chromatin, nascent RNA, translating mRNA and mature miRNA can be purified from specific cell populations. Specifically, we developed "Tagger" – a Cre and/or Flp recombinase-dependent mouse model that expresses four proteins to enable purification of distinct populations of cellular nucleic acids from specific cell types. Upon activation by cell type-directed recombinases, cells of a desired population express: 1) exogenous uracil phoshoribosyltransferase (UPRT) for tagging nascent total RNA with thiol groups upon administration of 4-thiouracil (4TU, TU-Tag), 2) epitope-tagged large ribosomal subunit protein 22 (Rpl22) to co-immunoprecipitate (co-IP) ribosome-bound mRNA (RiboTag), 3) epitope-tagged Argonaute 2 (Ago2, a component of the RNA-induced silencing complex) to co-IP mature miRNA (AgoTag), and 4) nucleus-directed mKate2 red fluorescent protein, providing good tissue penetrating transmission properties for in vivo imaging and a fluorescent nuclear tag (NucTag) for FACS enrichment of nuclei for chromatin studies. Overall design: For functional validation, Tagger mice were bred to neuron-directed Cre lines: vGluT2-Cre, Gad2-Cre and PV-Cre, producing vGluT2-Tagger, Gad2-Tagger and PV-Tagger mice, respectively. Then, TU-Tag RNA-seq, RiboTag RNA-seq, AgoTag small RNA-seq and NucTag MeDIP-seq from specific cell types and respective controls/input was generated.