Investigating the Context-Dependent Phase Separation of Human HOX Transcription Factors

Homeobox (HOX) transcription factors are essential for gene expression during embryonic development and hematopoiesis, and their dysregulation is potentially linked to several types of cancer. Recently, liquid-liquid phase separation (LLPS) has been proposed as a key mechanism in various physiological processes. Using computational tools and molecular dynamics (MD) simulations, we found that the human HOX transcription factors have a strong propensity to undergo phase separation. The large disordered regions of the HOX factors drive phase separation via a fly-casting like mechanism, where the terminal segments of the disordered regions extend out to interact with and draw in neighboring molecules. Also, formation of short transient secondary structures in the disordered regions was observed in MD simulations. The sequences of the transient structures match short linear motifs (SliMs), which are hotspots for interaction with partner molecules. Thus, the HOX transcription factors may act as scaffold proteins and recruit partner molecules, such as TALE proteins, in the biomolecular cocondensates, via interaction with these preformed structural elements. A total of 352 SliMs were mapped with the droplet-promoting disordered regions of the human HOX transcription factors, which indicated an abundance of possible binding sites. These results have been curated in an interactive webpage (https://pel.iitkgp.ac.in/) that generates motif maps, indicating the location of the motifs in the disordered regions of the HOX transcription factors. Overall, this work highlights the potential of phase separation of the human HOX factors, particularly through the lens of context-dependent interactions, which may lead to novel insights into HOX-related processes.