Genomic encoding of transcriptional burst kinetics

Mammalian gene expression is inherently stochastic(1,2)resulting in discrete bursts of RNA molecules synthesised from each allele(3–7). Although known to be regulated by promoters and enhancers, it is unclear how cis-regulatory sequences encode transcriptional burst kinetics. Characterization of transcriptional bursting, including the burst size and frequency, have mainly relied on live-cell(4,6,8) or single-molecule RNA-FISH(3,5,8,9) recordings of selected loci. Here, we inferred transcriptome-wide burst frequencies and sizes for endogenous genes using allele-sensitive single-cell RNA-sequencing (scRNA-seq). We show that core promoter elements affect burst size and uncover synergistic effects between TATA and Initiator elements, which were masked at mean expression levels. Importantly, we provide transcriptome-wide support for enhancers controlling burst frequencies and we additionally demonstrate that cell-type-specific gene expression is primarily shaped by changes in burst frequencies. Altogether, our data show that burst frequency is primarily encoded in enhancers and burst size in core promoters, and that allelic scRNA-seq is a powerful paradigm for investigating transcriptional kinetics.