Transcriptional bursting, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single cell RNA-seq

A time resolved nascent single-cell RNA-seq approach was developed to dissect gene-specific transcriptional bursting and the roles of SAGA and Mediator Tail (the activator-binding module). Most yeast genes show near-constitutive behavior while only a subset of genes show high mRNA variance suggestive of transcription bursting. Bursting behavior is highest in the coactivator redundant (CR) gene class (dependent on both SAGA and TFIID) and is strongest in TATA-containing CR genes. Applying this approach to analyze gene activation, we found that basal histone gene transcription is in a low level, low-noise constitutive mode while the activated state unexpectedly shows an increase in both the fraction of active promoters and a switch to a noisy and bursty transcription mode. Rapid depletion of either SAGA or Mediator Tail suggests that both factors play an important role in stimulating the fraction of active promoters at CR genes, with a variable gene-specific role in transcriptional bursting.