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

Abstract

Many transcription factors (TFs) localize in nuclear clusters of locally increased concentrations, but how TF clustering is regulated and how it influences gene expression is not well understood. Here, we use quantitative microscopy in living cells to study the regulation and function of clustering of the budding yeast TF Gal4 in its endogenous context. Our results show that Gal4 cluster formation is facilitated by, but does not completely depend on DNA binding and intrinsically disordered regions. Gal4 cluster properties are regulated by the Gal4-inhibitor Gal80 and Gal4 concentration. Moreover, we discover that clustering acts as a double-edged sword: self-interactions aid TF recruitment to target genes, but recruited Gal4 molecules that are not DNA-bound do not contribute to, and may even inhibit, transcription activation. We propose that cells need to balance the different effects of TF clustering on target search and transcription activation to facilitate proper gene expression.

A fine kinetic balance of interactions directs transcription factor hubs to genes

“…The increase in hub lifetimes at ectopic sites in the ZF5 mutant leads us to speculate that specific co-binding factor interactions are key to tuning the stability and frequency of hub interactions. Our results also highlight potential variability in the functional roles of hubs; for example, hub formation at one target may indeed lead to a loss of occupation at other sites leading to lower gene expression as has been observed in the case where hub function is assessed at an individual site ( 55 ).…”

Transcription Factor Condensates Mediate Clustering ofMETRegulon and Enhancement in Gene Expression

“…Consistent with this idea, a recent study reports that Gal4 condensation facilitates its recruitment to target genes but does not contribute to gene activation (Meeussen et al 2023). In human cells, artificially enhanced condensation of a TF Ews::Fli1 causes sequestering of this TF into the nucleolus, resulting in decreased expression of their target genes (Chong et al 2022).…”

“…It should be noted that more TF binding does not necessarily lead to an increase in gene expression level, for example, transcription may be limited by a step downstream of TF binding. Consistent with this idea, a recent study reports that Gal4 condensation facilitates its recruitment to target genes but does not contribute to gene activation (Meeussen et al 2023). In human cells, artificially enhanced condensation of a TF Ews::Fli1 causes sequestering of this TF into the nucleolus, resulting in decreased expression of their target genes (Chong et al 2022).…”

“…However, some reports studying TF condensates reveal a complex, sometimes contradictory, relation to gene expression, where the condensates are observed to have positive, negative, or neutral effects on transcription (Lu et al 2020;Lee et al 2021) . In a recent study of the GAL genes, for example, it is proposed that Gal4 condensation facilitates their recruitment to target genes but does not contribute to gene activation (Meeussen et al 2023). In general, the relation between TF condensates, multi-gene cluster, and gene regulation needs to be further studied.…”

Context transcription factors establish cooperative environments and mediate enhancer communication

“…More generally, condensate formation involves weak protein-protein interactions driven by intrinsically disordered domains that are present in both cofactors and TFs 27,32,33 . Finally, TF binding to DNA itself is critical as it catalyzes condensate formation 34,35 and directs the localization of RF clusters within cells 36 . Although there are several well-studied examples that underscore the importance of RF cluster formation and their subsequent size control for gene regulation 28,37,38 , it has proven difficult to disentangle which enhancers will give rise to RF clusters and which ones won't.…”