<scp>SET</scp> domain containing 3 ( <scp>SETD3</scp> ) interacts with bromodomain‐containing protein 2 ( <scp>BRD2</scp> ) and coordinates its chromatin association in mouse embryonic stem cells

Regulation of cell fate decisions during early embryonic development requires precise temporal and spatial control. The embryonic stem cell (ESC) transcription factor network maintains a delicate balance between self-renewal and differentiation by suppressing lineage-specific transcription while upregulating pluripotency factors. Our previous studies highlighted a critical role for the SET domain-containing protein actin-histidine N-methyltransferase (SETD3) in endoderm differentiation of mouse embryonic stem cells (mESCs). However, its specific functions within the nuclear context remained poorly understood. In this study, we used mass spectrometry to identify nuclear protein partners of SETD3. Our findings revealed that SETD3 interacts with the transcription factor CP2-like protein 1 (TFCP2L1; a pluripotency transcription factor) and bromodomain-containing protein 2 (BRD2) in the nucleus. Notably, our study highlights an essential role of SETD3 in the recruitment of BRD2 to chromatin in mESCs. Through domain deletions and proximity ligation assays, we established that this interaction is dependent on the RSB domain of SETD3 and potentially the BD2 domain of BRD2. The absence of SETD3 led to considerable alterations in the chromatin environment and a significant reduction in BRD2 recruitment, resulting in transcriptional changes. Our findings highlight the significant role of SETD3-dependent BRD2 recruitment in regulating chromatin dynamics and transcriptional outcomes in mESCs, enhancing our understanding of its role in ESC pluripotency exit and lineage commitment.