Ethanol stress induces transient restructuring of the yeast genome yet stable formation of Hsf1 transcriptional condensates

Reviewer #1 (Public Review):

Summary:
The study compares the transcriptional and epigenetic response of baker's yeast cells to heat shock and ethanol shock. The authors made several interesting observations. In response to heat shock, the transcription factor HSF1 rapidly forms foci, binds upstream elements of heat-shock-response genes, facilitates long-distance genomic contacts between heat-shock-response genes, and the genes are rapidly transcribed. In response to ethanol shock, the transcription factor HSF1 rapidly forms foci, binds upstream elements of heat-shock-response genes, facilitates long-distance genomic contacts between heat-shock-response genes, and yet transcription of the genes is substantially delayed. These insights are potentially important, as current models of eukaryotic gene control predict that physical contact between genes and regulatory elements is necessary, and in some cases sufficient to transcribe a gene. The current study indicates that the two effects are virtually decoupled in response to ethanol shock in yeast cells.

Overall, the conclusions appear appropriately supported by the data, and the data appear of high quality.

Strengths:
The particular strengths of the paper include an impressive combination of genomic and imaging-based approaches and insightful genetically engineered cell systems. The manuscript reports interesting and potentially important findings. The text is generally very well written, the ideas are clearly explained, and the reasoning is easy to follow.

Weaknesses:
The main weakness seems to be that the heat and ethanol shock approaches likely elicit pleiotropic effects, and therefore it is a challenge to test the causal relationship between various observations. Nevertheless, even as indirect effects might contribute to some of the authors' observations, the results are definitively worth reporting. Also, the presentation of some of the data could be improved.

Reviewer #2 (Public Review):

Significance
Rubio et al. study the behavior of the transcription factor Hsf1 under ethanol stress, examining its distribution within the nucleus and the coalescence of heat shock response genes in budding yeast. In comparison to the heat shock response, the response to ethanol stress shows similar gene coalescence and Hsf1 binding. However, there is a notable delay in the transcriptional response to ethanol, and a disconnect between it and the appearance of irreversible Hsf1 condensates/puncta, highlighting important differences in how Hsf1 responds to these two related but distinct environmental stresses.

Overview and general concerns
The authors studied how yeast responds to ethanol stress (8.5%) and compared it to the heat shock response (from 25{degree sign}C to 39{degree sign}C). They observed a more gradual increase in the expression of heat shock response (HSR) genes during ethanol stress compared to heat shock. Additionally, the recruitment of Hsf1 and Pol II to HSR genes, and the inter- and intrachromosomal interactions among these genes, showed slower kinetics under ethanol stress. They attribute the delay in transcriptional response to chromatin compaction induced by ethanol. Despite this delay, these interactions persisted longer. Hsf1 clusters, previously documented during the heat shock response, were also observed during ethanol stress and persisted for an extended period. The conditional degradation of Hsf1 and Rpb1 eliminated most inter- and intrachromosomal interactions for heat shock responsive genes in both ethanol stress and heat shock conditions, indicating the importance of these factors for long-distance interactions between HSR genes. Overall, this manuscript provides novel insights into the differential behavior of HSR genes under different stress conditions. This contributes to the broader understanding of how different stressors might elicit unique responses at the genomic and topographical level under the regulation of transcription factor Hsf1.

The central finding of the study highlights the different dynamics of Hsf1, Pol II, and gene organization in response to heat shock versus ethanol stress. However, one important limitation to consider is that the two chosen conditions may not be directly comparable. For a balanced assessment, the authors should ideally expose yeast to various ethanol concentrations and different heat shock temperatures, ensuring the observed differences stem from the nature of the stressor rather than suboptimal stress intensity. At the very least, an additional single ethanol concentration point on each side of 8.5% should be investigated to ensure that 8.5% is near the optimum. In fact, comparing the number of Hsp104 foci in the two conditions in Fig. 1E and F suggests that the yeast is likely experiencing different intensities of stress for the chosen heat shock condition and ethanol concentration used in this study.

A second significant concern is the use of the term "Hsf1 condensate". Chowdhary et al.'s 2022 Molecular Cell study highlighted an inhomogeneous distribution and rapid dynamics of Hsf1 clustering upon heat shock, with sensitivity to 1,6-hexandiol, which is interpreted as evidence for condensation by LLPS. However this interpretation has been criticized severely by McSwiggen et al. Genes Dev 2019 and Mussacchio EMBO J 2022. It is important to mention that 1,6-hexandiol is known to affect chromatin organization (Itoh et al. Life Science Alliance 2021). Describing such clusters as 'condensates' without further experimental evidence is premature. I encourage authors to settle on their neutral term 'puncta' which they use interchangeably with 'condensate' so as not to confuse the reader. The dynamic binding and unbinding of the low-abundance Hsf1 at coalescent chromatin target sites might explain the liquid-like properties of these clusters without the need for invoking the phase-separation hypothesis. While Hsf1 clusters exhibit features consistent with phase-separated condensates, other equally plausible alternative mechanisms, such as dynamic site-specific interactions (Musacchio, EMBO J, 2022), should also be considered. This is best left for the discussion where the underlying mechanism for puncta formation can be addressed.

Specific comments:

- Figure 1: Why does ethanol stress at 0 min display a larger number of Hsp104 foci per cell than heat shock at the same time? How are foci defined by the authors? In Fig. 1D, there are many smaller puncta. A comparative assessment of the number and size of foci for heat shock and ethanol stress would be beneficial.

- Figure 2: Selecting a housekeeping gene with consistent expression levels is crucial for meaningful qPCR analysis. Do SCR1 mRNA levels fluctuate during heat shock or ethanol stress? Additionally, certain genes, such as TMA10 and SSA4, lack visible bars at time 0. Are these levels undetectable? The varying y-axis scales are confusing; presenting data as relative fold changes could offer a clearer perspective.

- Line 239: The evidence for chromatin compaction is unconvincing. An increase in H3 occupancy by ChIP might indicate a reduction in histone exchange dynamics but may not relate to overall chromatin compaction. The authors use H2A-mCherry to suggest a decrease in chromatin volume, but this data is not persuasive. Did the authors observe any changes in nuclear size? Perhaps quantifying chromatin compaction more directly, using signal intensity per volume, would be informative.

- Line 340: The claim of a "strong spatiotemporal correlation" isn't evident from the data. Could correlation coefficients be provided? There is potential anti-correlation in Fig. 6 - Figure Supplement 1C.

- Figure 8: The WT data in Fig 8 seem inconsistent with Fig. 4 (e.g. the interaction frequency for HSP104 and SSA2). Are these fluctuations between experiments, or are they side effects of IAA treatment? The use of ethanol as an IAA solvent vehicle raises concerns. It would be beneficial if the authors could demonstrate that 1.7% ethanol in the control does not induce ethanol stress.

Reviewer #3 (Public Review):

This is an interesting manuscript that builds off of this group's previous work focused on the interface between Hsf1, heat shock protein (HSP) mRNA production, and 3D genome topology. Here the group subjects the yeast Saccharomyces cerevisiae to either heat stress (HS) or ethanol stress (ES) and examines Hsf1 and Pol II chromatin binding, Histone occupancy, Hsf1 condensates, HSP gene coalescence (by 3C and live cell imaging), and HSP mRNA expression (by RT-qPCR and live cell imaging). The manuscript is well written, and the experiments seem well done, and generally rigorous, with orthogonal approaches performed to support conclusions. The main findings are that both HS and ES result in Hsf1/Pol II-dependent intergenic interactions, along with the formation of Hsf1 condensates. Yet, while HS results in rapid and strong induction of HSP gene expression and Hsf1 condensate resolution, ES results in slow and weak induction of HSP gene expression without Hsf1 condensate resolution. Thus, the conclusion is somewhat phenomenological - that the same transcription factor can drive distinct transcription, topologic, and phase-separation behavior in response to different types of stress. While identifying a mechanistic basis for these results would be a tough task perhaps beyond the scope of this study, it would nevertheless be helpful to place these results in context with a series of other studies demonstrating across various organisms showing Hsf1 driving distinct activities dependent on the context of activation. Perhaps even more importantly, this work left out PMID: 32015439 which is particularly relevant considering that it shows that it is human HSF1 condensate resolution rather than simple condensate formation that is associated with HSF1 transcriptional activity - which is similar to the findings here with this particular dose of HS resulting in resolution and high transcriptional activity versus ES resulting in resolution failure and lower activity. It is also worth noting that the stresses themselves are quite different - ethanol can be used as a carbon source and so beyond inducing proteotoxic stress, the yeast are presumably adapting to this distinct metabolic state. Basically, it is not clear whether these differences are due to the dose of stress, versus we are looking at an early timepoint as ES initiates a genome-wide chromatin restructuring and gene expression reprogramming that goes beyond a response to proteotoxic stress. This reviewer is not suggesting a barrage of new experiments, but perhaps discussion points to contextualize results.