Heat Shock Factor 1 Drives Intergenic Association of Its Target Gene Loci Upon Heat Shock

Abstract

Transcriptional induction of Heat Shock Protein (HSP) genes in yeast is accompanied by dynamic changes in their 3D structure and spatial organization, yet the molecular basis for these phenomena remains unknown. Using chromosome conformation capture and single cell imaging, we show that genes transcriptionally activated by Heat Shock Factor 1 (Hsf1) specifically interact across chromosomes and coalesce into diffraction-limited intranuclear foci. Genes activated by the alternative stress regulators Msn2 and Msn4, in contrast, do not interact among themselves nor with Hsf1 targets.Likewise, constitutively expressed genes, even those interposed between HSP genes, show no detectable interaction. Hsf1 forms discrete subnuclear puncta when stressactivated, and these puncta dissolve in concert with transcriptional attenuation, paralleling the kinetics of HSP gene coalescence and dissolution. Nuclear Hsf1 and RNA Pol II are both necessary for intergenic HSP gene interactions, while DNA-bound Hsf1 is necessary and sufficient to drive coalescence of a heterologous gene. Our findings demonstrate that Hsf1 can dynamically restructure the yeast genome.

Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome

“…Hsf1-target genes engage in frequent intergenic (both cis- and trans- ) interactions during acute heat shock; such coalescence is strictly dependent on Hsf1 and encompasses High NHS, Intermediate NHS, and Low NHS genes (Chowdhary et al. , 2017, 2018). HSP gene coalescence may be indicative of liquid–liquid phase separation postulated to underlie transcriptional control in higher eukaryotes (Hnisz et al.…”

“…3) Hsf1 expands its target regulon during heat shock by cooperating with CRCs to reveal HSEs occluded by nucleosomes, concomitant with driving its target genes—dispersed throughout the genome—into a coalesced, potentially phase-separated, state (Chowdhary et al. , 2017, 2018). Together, these mechanisms allow cells to dynamically control the breadth and magnitude of the heat shock response to tune the proteostasis network according to need.…”

“…Recently, Hsf1-regulated yeast genes were observed to undergo striking alteration in their local structure and engage in highly specific cis- and trans -intergenic interactions on their transcriptional activation, coalescing into discrete intranuclear foci (Chowdhary et al. , 2017, 2018).…”

Mechanisms of Interplay between Transcription Factors and the 3D Genome

“…However, in most cases, whether oligomerization per se shapes 3D genome organization is unclear. In heat-shocked yeast, the heat shock response protein Hsf1 mediates clustering of Hsf1 target genes (Chowdhary et al, 2019), but whether Hsf1's ability to form trimers mediates these contacts remains uncertain. Similarly, YY1 and CTCF are implicated in the transient homolog pairing of the X inactivation centers in differentiating mouse ES cells, where the role of CTCF is presumably unrelated to loop extrusion, which is thought to act on individual chromosomes rather than on pairs of chromosomes (Xu et al, 2007).…”

Shugoshin 2—a new guardian for heat shock transcription

“…Is there cell‐type specificity of coactivators? What role do coactivators play in the HSF1‐driven 3D architecture of HSP genes (Chowdhary et al , )? What role do coactivators play in HSF1's activity in disease states?…”