Transcriptional architecture and Pol II regulation at promoters, enhancers, and enhancer clusters in Canis lupus familiaris

Domestic dog exhibits remarkable phenotypic diversity and provides versatile models for genomics, evolution, and complex traits. DNA sequences and stable RNAs have revealed regulatory regions in the dog genome. However, transcriptional activity, regulatory architecture, and control of RNA Polymerase II (Pol II) across genes and enhancers remain uncharacterized. Here, we track transcription at nucleotide-resolution, measure RNA expression and stability, and analyse mechanisms of Pol II regulation in golden retriever macrophages. We report the precise architectures of promoters, enhancers, and enhancer clusters, and quantify Pol II progression from the initiation, through the pause-region, into elongation and termination. Triggering transcriptional change by heat stress reveals instant reprogramming of genes via promoter-proximal pause-regulation and enhancers via initiation. Enhancers within a cluster mount a unified response. This study identifies functional genomic regions de novo , characterizes transcriptional architectures of genes, enhancers, and enhancer clusters, quantifies RNA synthesis and stability, and reveals mechanisms of transcription in Canis lupus familiaris .