Cell-type specific RNA Pol II activity maps in intact-tissues: Gateway to mammalian gene regulatory mechanisms in vivo

Summary: Abstract Body: Accessing ongoing RNA Pol II activity in specific cell-types within intact-tissues can dissect regulatory mechanisms of development. Here, we create Cre-inducible mice for cell-type-specific GFP tagging of endogenous Pol II. Transcriptional run-on on intact-tissue chromatin followed by GFP-immunoprecipitation (our PReCIS-seq method) maps the transcriptionally-engaged Pol II genome-wide on proximal-promoters, gene bodies, and active enhancers. Using keratinocytes of intact-skin as a model, we demonstrate that all transcriptionally regulated functions of a homeostatic transition employ Pol II promoter-recruitment and promoter-proximal pause-release mechanisms. A global Pol II regulatory polarization - enabling contrasting modulation of cellular safeguarding and lineage identity gene expression - is maintained from embryonic development through adult homeostasis. This polarization appears hard-wired in two proximal-promoter structures that distinguish high-paused genes with restricted pause-release from low-paused genes undergoing rapid Pol II firing into productive elongation. PReCIS-seq provides unprecedented in vivo access to Pol II regulatory mechanisms in mammalian development, homeostasis, and disease. Tudorita Tumbar¹, Gopal Chovatyia¹, Chris Ke Bai¹ 1. Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States. Genetic Disease, Gene Regulation, Gene Therapy & Epigenetics