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

Chowdhary, Surabhi; Kainth, Amoldeep S.; Pincus, David; Gross, David S.

doi:10.1016/j.celrep.2018.12.034

Cited by 66 publications

(51 citation statements)

References 49 publications

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“…Confocal imaging was performed at the Nikon Imaging Center at the Whitehead Institute for Biomedical research using the Andor spinning disc system as previously described (23). Heat shock was performed on live cells using an objective heater as described (24). Hsc82 is the yeast homolog of Hsp90.…”

Section: Confocal Imagingmentioning

confidence: 99%

“…First, the clients that titrate Hsp70 away upon heat shock are thought to be primarily nascent proteins emerging from ribosomes in the in the cytosol (15). Yet, Hsf1 activates target gene transcription in the nucleus in less than a minute following heat shock (24). How do cytosolic clients titrate away nuclear Hsp70 so quickly, especially given that the molecular ratio of Hsp70:Hsf1 in yeast cells exceeds 1000:1 (25)?…”

Section: Introductionmentioning

confidence: 99%

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Subcellular localization of the J-protein Sis1 regulates the heat shock response

Feder

Ali

Singh

et al. 2020

Preprint

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One sentence summary: Localization of the J-protein Sis1 to a subcellular network of proteostasis factors activates the heat shock response. ABSTRACT Cells exposed to heat shock induce a conserved gene expression program -the heat shock response (HSR) -encoding chaperones like Hsp70 and other protein homeostasis (proteostasis) factors. Heat shock also triggers proteostasis factors to form subcellular quality control bodies, but the relationship between these spatial structures and the HSR is unclear.Here we show that localization of the J-protein Sis1 -a co-chaperone for Hsp70 -controls HSR activation in yeast. Under nonstress conditions, Sis1 is concentrated in the nucleoplasm where it promotes Hsp70 binding to the transcription factor Hsf1, repressing the HSR. Upon heat shock, Sis1 forms an interconnected network with other proteostasis factors that spans the nucleolus and the surface of the cortical ER. We propose that localization of Sis1 to this network directs Hsp70 activity away from Hsf1 in the nucleoplasm, leaving Hsf1 free to induce the HSR.In this manner, Sis1 couples HSR activation to the spatial organization of the proteostasis network. degradation (ERAD) (43). Together these images show that Sis1 colocalizes with RQC during heat shock.Beyond colocalization during heat shock, the 3D reconstructions of the lattice light sheet images revealed that Sis1-YFP, Hsp104-BFP, Rpn1-mScarlet, Ltn1-mScarlet and Cdc48-mScarlet form a semi-contiguous network ( Figure 5A-C). Sis1-YFP and Rpn1-mScarlet form an overlapping and highly ordered network that connects the nucleolar ring with a series of cytosolic foci ( Figure S4A, B, Movie S2). Hsp104 is excluded from the nucleolar ring but colocalizes with Sis1 and Rpn1 in the cytosolic network. Hsp90 (Hsc82-mScarlet) does not appear to participate in the network nor in any other Sis1-containing structures ( Figure S4C).The ER has been previously implicated as an organizational factor for the spatial arrangement of protein quality control factors, including Hsp104 (27,44). Moreover, we found that the ER structural protein Rtn1 co-precipitated with Sis1-3xFLAG during heat shock. To test if the Sis1 cytosolic network forms in proximity to the ER, we imaged Rtn1-mScarlet in cells expressing Sis1-YFP and Hsp104-BFP. Indeed, Sis1-YFP increased its signal overlap with Rtn1-mScarlet from MOC = 0.13 under nonstress conditions to MOC = 0.60 during heat shock ( Figure 5D), suggesting increased association with the ER. Space-filling 3D cell projections reveal the orientation of the interaction network, with Rtn1 toward the periphery and Sis1 and Hsp104 lining the interior ( Figure 5E). The imaging data suggest that Sis1 forms a highly connected network with the proteasome and RQC on the surface of the ER.Lastly, we tested if Sis1 is required for the proteasome to re-localize to the nucleolar ring during heat shock. To this end we anchored away Sis1 prior to heat shocking cells and monitored localization of Rpn1-mScarlet and Hsp104-BFP. Following Sis1 anchor away, we found that Rpn...

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Section: Confocal Imagingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Subcellular localization of the J-protein Sis1 regulates the heat shock response

Feder

Ali

Singh

et al. 2020

Preprint

Self Cite

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“…In doing so, this study goes beyond correlation and directly establishes the causal function of chromosome topology in this process. In yeast, chromosome conformation was also thought to affect transcription 17,[39][40][41][42] and DNA replication 43 . In the future, CICI can be used to study these 3D genome functions.…”

Section: Fig 2d and E)mentioning

confidence: 99%

“…In addition, proteins that set up chromosome interactions may also directly participate in genomic processes. For example, the looping between the Locus Control Region (LCR) enhancer and the β -globin promoter is established by transcription factors GATA1, FOG1, KLF1 and Ldb1 [14][15][16] ; the clustering of GAL genes or heat-shock genes requires transcription factor Gal4 or Hsf1 17,18 . Mutations of these factors will result in simultaneous loss of chromosomal interactions and gene expression, preventing us from elucidating the relation between them.…”

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confidence: 99%

Chemically Induced Chromosomal Interaction (CICI): A New Tool to Study Chromosome Dynamics and Its Biological Roles

Zou

Yan

et al. 2020

Preprint

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Numerous intra-and inter-chromosomal contacts have been mapped in eukaryotic genomes, but it remains challenging to link these 3D structures to their regulatory functions. To establish the causal relationships between chromosome conformation and genome functions, we need a method that allows us to selectively perturb the conformation at targeted loci. Here, we developed a method in budding yeast, Chemically Induced Chromosomal Interaction (CICI), to engineer long-distance chromosomal interactions selectively and dynamically. We implemented CICI at multiple intra-and inter-chromosomal loci pairs and showed that CICI can form in >50% of cells, even between loci with very low Hi-C contact frequencies. CICI formation is slower at these low Hi-C sites, revealing the dynamic nature of the Hi-C signals.As a functional test, we forced the interaction between mating-type locus (MAT) and HMR and observed significant change in donor preference during mating-type switching, showing that chromosome conformation plays an important role in homology-directed DNA repair. Overall, these results demonstrate that CICI is a powerful tool to study chromosome dynamics and the 3D genome function.

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“…The alteration of chromatin spatial structure, e.g, the genome compartments (Lieberman-Aiden et al, 2009b), the topological associated domains (TAD) (Dixon et al, 2012), and chromatin loops (Rao et al, 2014), has been suggested underling the transcriptional responses to HS in multiple species. In yeast, up-regulated HSP genes undergo dynamic alteration in their 3D genome structure (Chowdhary et al, 2017;Chowdhary et al, 2019). In Drosophila, HS induces relocalization of architectural proteins from TAD borders to inside TADs, and causes a dramatic rearrangement in the 3D organization of chromatin .…”

Section: Introductionmentioning

confidence: 99%

Widespread transcriptional responses to the thermal stresses are prewired in human 3D genome

Wang

et al. 2019

Preprint

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Temperature changes is one of the most common environmental stress that consequences with massive phenotypic responses for almost all the life forms. The dysregulation of heat shock (HS) response genes had been found associated with various severe diseases, including cancer. Although the HS response has been well studied in animal cells, it remains elusive whether or not the cells response to cold shock (CS) similarly. Here, we comprehensively compared the changes of gene expression, epigenetic marks (H3K4me3 and H3K27ac), binding of genome architecture proteins (CTCF, SMC3 and Pol II) and chromatin conformation after HS and CS in human cells. Widespread expression change was observed after both HS and CS. Remarkably, we identified distinguished characters in those thermal stress responded genes at nearly all levels of chromatin architecture, i.e, the compartment, topological associated domain, chromatin loops and transcription elongation regulators, in the normal condition. However, the global chromatin architecture remains largely stable after both CS and HS. Interestingly, the thermal stresses responded genes are prone to spatial clustering even before the temperature changes.Our data suggested that the transcriptional response to the thermal stresses maybe independent to the changes of the high-level chromatin architecture, e.g., compartments and TAD, while it may be more dependent on the precondition of the chromatin and epigenetic settings at the normal condition.

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

Cited by 66 publications

References 49 publications

Subcellular localization of the J-protein Sis1 regulates the heat shock response

Subcellular localization of the J-protein Sis1 regulates the heat shock response

Chemically Induced Chromosomal Interaction (CICI): A New Tool to Study Chromosome Dynamics and Its Biological Roles

Widespread transcriptional responses to the thermal stresses are prewired in human 3D genome

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