Understanding the precise functions and relationship of BRD2 with other bromodomain and extraterminal motif (BET) proteins is central for the application of BET-specific and pan inhibitors. Here, we used acute protein degradation and quantitative genomic and proteomic approaches to investigate the primary functions of BRD2 in transcription. We report that BRD2 is required for TAF3-mediated Pol II initiation at low levels of H3K4me3-modified promoters and Pol II elongation by suppressing R-loops. Single and double depletion revealed that BRD2 and BRD3, but not BRD4, redundantly and independently function in Pol II transcription at different promoters and cooperatively occupy enhancers. Interestingly, we found that depletion of BRD2 affects the expression of different genes during differentiation processes, priming with promoter regulation in ES cells. Therefore, our results suggest complex interconnections between BRD2 and BRD3 at promoters to fine-tune Pol II initiation and elongation for control of cell state. Overall design: We have finished the ChIA-PET, ChIP-seq, RNA-seq and 4C-seq to investigate the roles of BRD2 in transcription initiation. The V6.5 mouse ES (mES) cell line was used to perform all the high-throughput analysis. BRD2-degron mES cells were pre-treated with 1 μg/ml doxycycline for 18 hours and treated with or without 500 μM indole-3-acetic acid for 24 hours.