Cell-type-specific RNA Pol II activity maps in intact-tissues: gateway to mammalian gene regulatory mechanisms in vivo [CUT&RUN]

Accessing ongoing RNA Pol II activity in specific cell types within intact-tissue is critical to reveal regulatory mechanisms of development. We developed PReCIS-seq, a method combining Cre-inducible GFP-tagging of endogenous Pol II with transcriptional run-on and GFP-immunoprecipitation, to map transcriptionally-engaged Pol II genome-wide in targeted cell types of mouse tissues. Applied to keratinocytes within intact-skin, PReCIS-seq demonstrates that transcriptionally activated functions of biological transitions generally employ both Pol II promoter-recruitment and promoter-proximal pause-release mechanisms. We uncover a global Pol II regulatory polarization that modulates cellular safeguarding versus lineage identity genes across embryonic development to adult homeostasis. This polarization is associated with distinct proximal-promoter structures distinguishing high-paused genes with restricted Pol II pause-release from low-paused genes undergoing rapid Pol II firing into productive elongation. PReCIS-seq also identifies active enhancers based on divergent transcription. This approach enables high-resolution, cell-type-specific analysis of Pol II dynamics in intact-tissues across mammalian development, homeostasis, and disease.