BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae (RNA-Seq)

Human BET family members are promising targets in the therapy of cancer and immunoinflammatory diseases, but their mechanism of action and functional redundancies are poorly understood. Yeast BET factors Bdf1/2 were previously proposed to act as anchors for coactivator TFIID. We investigated their genome wide roles in transcription and found that, while they cooperate with TFIID at many genes, their contributions to transcription are often significantly different. Bdf1/2 co-occupy the majority of yeast promoters and affect preinitiation complex formation by participating in recruitment of TFIID, Mediator and basal factors to chromatin. Surprisingly, we discovered that hypersensitivity of genes to Bdf1/2 depletion results from combined defects in initiation of transcription and early elongation. Bdf1/2 are critical components of yeast transcriptional machinery with many functional similarities to human BET proteins, most notably Brd4. Overall design: Newly synthesized RNAs were labeled with 4-thioU, purified and analyzed with RNA-seq. Depletion of selected factors was achieved either thorugh targeted degradation (auxin-degron system) or deletion of BDF2 gene. Corresponding control and treatment sample files are labeled DMSO and IAA (3-indolacetic acid), respectively. All experiments were done in two (A,B) or three replicates (A,B,C).