Modulating gene regulation function by chemically controlled transcription factor clustering

Abstract

Recent studies have suggested that transcriptional protein condensates (or clusters) may play key roles in gene regulation and cell fate determination. However, it remains largely unclear how the gene regulation function is quantitatively tuned by transcription factor (TF) clustering and whether TF clustering may confer emergent behaviors as in cell fate control systems. Here, to address this, we construct synthetic TFs whose clustering behavior can be chemically controlled. Through single-parameter tuning of the system (i.e., TF clustering propensity), we provide lines of evidence supporting the direct transcriptional activation and amplification of target genes by TF clustering. Single-gene imaging suggests that such amplification results from the modulation of transcriptional dynamics. Importantly, TF clustering propensity modulates the gene regulation function by significantly tuning the effective TF binding affinity and to a lesser extent the ultrasensitivity, contributing to bimodality and sustained response behavior that are reminiscent of canonical cell fate control systems. Collectively, these results demonstrate that TF clustering can modulate the gene regulation function to enable emergent behaviors, and highlight the potential applications of chemically controlled protein clustering.

Gene activation guided by nascent RNA-bound transcription factors

“…Previous studies have suggested that TF concentration regulates transcriptional bursting kinetics 26 , 43 , 77 . Moreover, strong enhancers drive bursts at a higher frequency than weak enhancers, while SEs exhibit similar bursting patterns to strong enhancers, showing relatively longer burst duration and higher burst amplitude 23 , 78 .…”

“…Our work suggests that the awareness of RNA bifunctionality is not only of conceptual importance, but will be increasingly useful when nascent RNA acts as a general binding platform to recruit transcription regulators. Previous studies have suggested that TF concentration regulates transcriptional bursting kinetics 26,43,77 . Moreover, strong enhancers drive bursts at a higher frequency than weak enhancers, while SEs exhibit similar bursting patterns to strong enhancers, showing relatively longer burst duration and higher burst amplitude 23,78 .…”

Transcription factor clusters enable target search but do not contribute to target gene activation

“…Moreover, an important open question is how clustering influences TFs during the different steps of transcription activation 13,[21][22][23] . Clustering and IDR-mediated interactions have been reported to enhance target search (increasing the DNA binding rate) [24][25][26][27][28] , to increase the local concentration of TFs at the promoter (increasing the DNA binding rate), to stabilize TF binding to DNA (decreasing the rate of TF unbinding) 12 , to enable 3D genomic interactions between target genes 29 and to boost transcription activation through enhanced recruitment of cofactors and polymerase molecules 30,20,16,31,32 . In contrast, clustering of synthetic TFs and the oncogenic TF EWS::FLI1 instead inhibit gene expression 33,34 .…”

STRIP2 motivates non-small cell lung cancer progression by modulating the TMBIM6 stability through IGF2BP3 dependent

“…The control primers for human RPL30 were provided with the kit. The process of RT-qPCR was carried out according to described previously [26,27] .…”