Transcriptional architecture of promoters and enhancers and the rapid unleash of heat shock response in Canis lupus familiaris [PRO-seq]

Dogs exhibit high genetic diversity due to extensive breeding, and provide a versatile model for genetics, evolution, and complex traits. While RNA synthesis and transcriptional architecture of promoters and enhancers have been extensively analyzed in human, mouse, and fly, little is known about the mechanisms that coordinate gene and enhancer transcription in dog. Here, we combine precision run-on sequencing (PRO-seq) and strand-specific mRNA-seq (mRNA-seq) to measure nascent transcription, mRNA expression and mRNA stability in golden retriever macrophage (DH82) cells. Tracking transcription at nucleotide-resolution uncovers the precise transcription start nucleotides (TSN) genome-wide, identifies the exact locations of promoters and transcribed enhancers, and quantifies transcription machineries at initiation, promoter proximal pause, gene bodies, and termination windows. Moreover, we trigger an instant transcriptional reprogramming using heat shock, and track at nucleotide-resolution, how dog cells coordinate RNA synthesis and mRNA expression across the genome. Taken together, this study describes the transcriptional landscape at nucleotide-resolution, measures RNA synthesis, mRNA expression and mRNA-stability, and identifies mechanisms of gene and enhancer reprogramming in Canis lupus familiaris. Overall design: Precision run-on sequencing (PRO-seq) of macrophage-like cells from golden retriever (DH82) under normal growth conditions and heat shock.