Our research focuses on human transcription factor (TF) protein interactions and close protein environment. TFs are proteins that control gene expression by recruiting transcription cofactors to regulate not only transcription itself but also the epigenetic landscape and access to the genomic DNA. One of the outstanding challenges, and point of interest, in the study of TFs and their cofactors is that these interactions occur in context of phase separation. Phase separation forms dynamic aggregates of proteins and RNA where both contribute to the interactions within the aggregate. Phase separation is typically initiated by intrinsically disordered regions (IDRs), which are found in many TF effector regions.
We use biotin proximity labeling (BioID) to study the human TFs in the HEK293 model system. BioID detects both stable and transient protein interactors by biotinylating nearby protein cysteine residues from the tagged TF of interest. This method can capture dynamic and mobile protein constituents of phase separation aggregates. The resulting complex protein samples are analyzed using mass spectrometry.
By thoroughly examining the interactions of human TFs on a large scale, we can identify the mechanisms and roles of individual TFs, the cofactors they interact with and potential interactions with other TFs. By analyzing the TF IDRs and interactors, we can also start to understand how particular IDR sequences govern specific interactions in the cell.