Transcription Factor Condensates Mediate Clustering of MET Regulon Genes and Enhance Their Gene Expression

Основні поняття

Transcription factor Met4 and its co-activator Met32 form liquid-liquid phase separated condensates in yeast nuclei upon methionine depletion. These condensates co-localize with and mediate the 3D clustering of their target genes, leading to enhanced transcriptional activity of the clustered genes.

Анотація

The study investigates the role of transcription factor (TF) condensates in 3D genome organization and gene regulation, using the methionine (met) response pathway in budding yeast as a model system.
Key findings:

The TFs Met4 and Met32 form puncta-like structures in yeast nuclei upon met depletion, indicating they can undergo liquid-liquid phase separation (LLPS) and form condensates.
Purified Met32 can form condensates with LLPS properties in vitro, and it can co-condense with Met4.
The loci bound by Met4 and its co-activators co-localize with the Met4 puncta in vivo.
A subset of Met4 target genes cluster in 3D nuclear space in a Met4-dependent manner.
Genomic loci near endogenous Met4 binding sites, up to 40kb away, show enhanced transcriptional activity of a reporter gene, forming "transcriptional hotspots".
A Met4 mutant with a partial deletion of an intrinsically disordered region, which reduces Met4 puncta formation, selectively decreases the reporter activity at the hotspot loci.

These results support a model where Met4 and Met32 form condensates that mediate the 3D clustering of their target genes, leading to elevated local concentrations of transcription-related factors and enhanced gene expression.

Статистика

Met4 and Met32 form puncta-like structures in yeast nuclei upon methionine depletion.
Met32 forms condensates with LLPS properties in vitro, and it can co-condense with Met4.
Loci bound by Met4 and its co-activators co-localize with the Met4 puncta in vivo.
A subset of Met4 target genes cluster in 3D nuclear space in a Met4-dependent manner.
Genomic loci near endogenous Met4 binding sites show enhanced transcriptional activity of a reporter gene, forming "transcriptional hotspots".
A Met4 mutant with a partial deletion of an intrinsically disordered region reduces Met4 puncta formation and selectively decreases the reporter activity at the hotspot loci.

Цитати

"Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion."
"Purified Met32 forms condensates with LLPS properties in vitro, with which Met4 can merge."
"The loci that are associated with the Met TFs co-localize with the Met4 puncta, and at least a subset of Met4 target genes cluster in 3D nuclear space in a Met4-dependent manner."
"The MET3pr-GFP reporter inserted near the endogenous Met4 target sites shows higher enrichment of Met TFs / Pol II and enhanced transcriptional activity (hotspots)."
"A Met4 IDR truncation that reduces Met4 puncta formation selectively affects the reporter activity at hotspots."

Ключові висновки, отримані з

Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression

by Lee,J., Simp... о www.biorxiv.org 02-08-2024

https://www.biorxiv.org/content/10.1101/2024.02.06.579062v1

Глибші Запити

How do the properties and dynamics of TF condensates, such as size, fluidity, and residence time, influence their ability to mediate gene clustering and transcriptional regulation?

TF condensates play a crucial role in mediating gene clustering and transcriptional regulation through their unique properties and dynamics. The size of TF condensates is essential as it determines the spatial organization of the associated genes. Larger condensates can accommodate multiple target genes, bringing them into close proximity for coordinated regulation. The fluidity of TF condensates allows for dynamic interactions with chromatin and other cellular components, facilitating rapid gene activation or repression in response to environmental cues. The residence time of TFs within condensates influences the duration of gene expression, with longer residence times leading to sustained transcriptional activity. Overall, the properties and dynamics of TF condensates contribute to the spatial and temporal regulation of gene expression by facilitating gene clustering and coordinating transcriptional responses.

What other cellular factors or mechanisms, besides TF condensates, may contribute to the formation and maintenance of co-regulated gene clusters?

In addition to TF condensates, several other cellular factors and mechanisms may contribute to the formation and maintenance of co-regulated gene clusters. Chromatin architecture, including the presence of enhancer-promoter loops and topologically associating domains (TADs), can play a role in bringing co-regulated genes into spatial proximity. Chromatin remodeling complexes and histone modifications also contribute to the accessibility of gene regulatory regions, influencing gene clustering. Transcriptional co-activators and co-repressors, as well as RNA polymerase II and other transcriptional machinery components, participate in the assembly and maintenance of gene clusters. Nuclear organization, such as the positioning of genes relative to nuclear compartments like the nucleolus or nuclear pores, can also impact gene clustering. Additionally, signaling pathways and post-translational modifications of TFs and chromatin-associated proteins may regulate the formation and stability of co-regulated gene clusters.

Could the principles of TF condensate-mediated gene regulation discovered in the yeast methionine response pathway be applied to understand transcriptional regulation in other stress response or developmental pathways in higher eukaryotes?

The principles of TF condensate-mediated gene regulation discovered in the yeast methionine response pathway can indeed be applied to understand transcriptional regulation in other stress response or developmental pathways in higher eukaryotes. The concept of TF condensates facilitating gene clustering, enhancing local TF concentrations, and coordinating transcriptional responses is likely to be conserved across different organisms and pathways. In stress response pathways, such as heat shock or osmotic stress, TF condensates may play a similar role in organizing stress-responsive genes and promoting their rapid activation. In developmental pathways, TF condensates could contribute to the spatial and temporal regulation of gene expression during morphogenesis and differentiation. By studying the dynamics and properties of TF condensates in various cellular contexts, researchers can gain insights into the mechanisms underlying transcriptional regulation in higher eukaryotes and potentially uncover novel therapeutic targets for diseases related to dysregulated gene expression.