Genome-Wide Transcription Burst Size Quantification through 4sUDRB Sequencing

Transcription bursting is a substantial source of gene-expression noise for many genes, contributing to phenotypic heterogeneity and potentially driving both physiological and pathological processes such as tumorigenesis and drug resistance. Characterising bursting dynamics at a genome-wide scale has been incomplete however as it has been restricted to inferring bursts in mRNA formation computationally from the heterogeneity of mRNA levels in single cell transcriptomic data. Here, we measured the bursting of transcription for GREB1 in single MCF-7 cells and used this to calibrate genome-wide measurements from 4sUDRB sequencing. Comparing across the genome, we find a significant trend in which the transcription burst sizes range from 1 to ~200 and attributes to ~85% of the steady state expression level, while the burst frequency attributes minimally. Individual genes deviate strongly from this trend and engage both in anomalous burst size and in anomalous burst frequency. We find that presence of the TATA box or Inr sequence within gene promoters significantly predicts a larger burst size, as does a promoter associated YY1 transcription factor binding motif. We also reveal several epigenetic marks to be strongly associated with transcription burst size, such as H3K79me2 and H3K14ac. This method paves the way to accurately quantify transcription dynamics genome-wide in various cell types to elucidate the mechanistic role of cell-type specific epigenetic gene regulation.