The Gross lab has been awarded a 4-year, $1.2 million grant from the National Institute of General Medical Sciences (NIGMS) for a project entitled "Genome Architecture and Gene Control in Response to Stress."
David S. Gross, PhD
Professor of Biochemistry & Molecular Biology
David Gross hails from Denver, Colorado and received his BA from Northwestern University and his PhD from the University of Colorado. Following his postdoctoral studies at the University of Texas Health Science Center in Dallas, David joined the faculty of the Louisiana State University Health Sciences Center, where he has been a member of the Department of Biochemistry and Molecular Biology since the late 1980’s. His work has always focused on one question: How are genes precisely and dynamically regulated in the context of their natural chromatin environment? His lab has been continuously funded by either the National Institutes of Health or National Science Foundation (or both) for nearly three decades. David’s passion for science, combined with the enjoyment he receives in training students and postdocs, makes him feel quite lucky to have the job that he has. He also enjoys cycling, traveling and barbecuing vegan food. David and his wife, Susan, have two daughters, Rachel and Sarah, who live in Milwaukee and Brooklyn, respectively, and two grandchildren, Leonardo and Simona.
Special Methods Issue edited by S. Chowdhary, A.S. Kainth and D.S. Gross that features a palette of powerful techniques for mapping chromatin topology and 3D genome organization. Each technique described in this issue is represented on the cover.
Third-year graduate student Linda S. Rubio was awarded Biochemistry Graduate Student of the Year at Graduate Research Day, April 26, 2019. Linda is a member of the Gross Lab and follows in the footsteps of two other PhD students from that lab.
Paper accepted in Cell Reports. Title: Heat Shock Factor 1 Drives Intergenic Association of Its Target Gene Loci Upon Heat Shock.
Congratulations to Principal Investigator Dr. David Gross for being awarded an R15 AREA grant entitled, “Chromosomal Conformation and Nuclear Organization of Heat Shock Protein Genes.” The grant provides Dr. Gross with $100,000 per year each year for three years.
Major Research Interests:
The goal of our NIH- and NSF-funded research program is to dissect the molecular mechanisms by which the transcription of protein-encoding genes is regulated. A central focus is the gene-specific activator Heat Shock Factor 1 (Hsf1), master regulator of the eukaryotic heat shock response. Hsf1 regulates the expression of genes that encode molecular chaperones and other cytoprotective Heat Shock Proteins (HSPs). We have discovered that in the yeast, Saccharomyces cerevisiae, Hsf1 binds to the enhancer/UAS regions of a core group of ~50 genes whose heat shock-induced transcription is strongly dependent on this protein. Its constitutive binding to a subset of these genes is enhanced by cooperative interactions with ‘pioneer’ transcription factors and chromatin remodeling complexes. Moreover, Hsf1 acts in concert with Mediator, a conserved coactivator complex, in driving its transcriptional program.
Recently, our laboratory made the striking observation that Heat Shock Protein (HSP) genes under the control of Hsf1 undergo profound conformational changes upon their heat-induced transcriptional activation. These genes form chromatin loops between their 5’- and 3’-ends, engage in concerted intragenic contacts and most strikingly, coalesce into discrete intranuclear foci through both intra- and interchromosomal interactions. Such chromatin contacts strongly correlate with the instantaneous rate of HSP gene transcription and lead to a dramatic restructuring of the yeast genome. Genome restructuring is critically dependent on at least two proteins, DNA-bound Hsf1 and transcriptionally engaged RNA Polymerase II. Genes regulated by alternative transcription factors, even those responsive to heat shock or interposed between HSP genes, do not coalesce. Our data suggest that Hsf1, likely in combination with other factors (currently under investigation), drives its target loci into a phase-separated state whose assembly is highly dynamic and critically required for the robust expression of HSP genes, and by extension, cell survival under conditions of acute thermal stress.
In this piece we argue that HSP gene coalescence shares key attributes with mammalian super-enhancers including exceptional concentration of transcription factors and coactivators, extensive DNA looping and clustering, and cooperative assembly into phase-separated condensates.
- Chromosome Conformation and 3D Nuclear Architecture of Heat Shock Protein (HSP) Genes
- Genome-wide Organization of HSP Genes and Identification of Molecular Determinants Underlying the Formation of Transcription Factories
- Role of Mediator in the Transcriptional Regulation and 3D Genomic Organization of Hsf1 Target Genes
- Genetic and Epigenetic Determinants of Heat Shock Factor 1 Occupancy
Chromosome Conformation and 3D Nuclear Architecture of Heat Shock Protein (HSP) Genes
Participants: Surabhi Chowdhary and Amoldeep S. Kainth
Three-dimensional chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. In this project, we are using chromosome conformation capture (3C) in combination with fluorescence microscopy to study the chromosome conformation and 3D nuclear architecture of Heat Shock Factor 1 (Hsf1)-regulated HSP genes in the budding yeast Saccharomyces cerevisiae. We have discovered the existence of dramatic intragenic folding interactions that occur between UAS and promoter, promoter and terminator (gene ‘looping’), and regulatory and coding regions (gene ‘crumpling’) of these genes following exposure to heat. Such interactions are prominent within 60 sec of thermal upshift, peak within 2.5 min and attenuate by 30 min. They tightly correlate with HSP gene transcriptional activity. With similar kinetics and dynamics, HSP genes engage in intra- and interchromosomal interactions involving their UAS, promoter, coding and terminator regions, coalescing into discrete intranuclear foci. Genes regulated by an alternative stress-inducible activator, Msn2/Msn4, loop and crumple in response to heat shock yet interestingly do not coalesce. This work provides evidence for novel transcription-dependent gene ‘crumpling’ and demonstrate the de novo assembly and disassembly of transcriptionally active foci.
Chowdhary, S., Kainth, A.S. and Gross, D.S. 2017. Heat Shock Protein genes undergo dynamic alteration in their three-dimensional structure and genome organization in response to thermal stress. Mol. Cell. Biol. 37: e00292-17.
Chowdhary, S., Kainth, A.S. and Gross, D.S. 2019. Chromosome conformation capture that detects novel cis- and trans-interactions in budding yeast. Methods, Epub ahead of print.
Left: Circos plot summarizing intragenic interaction frequencies detected within HSP genes in 10 min heat shocked (HS) cells. Similar looping and folding interactions have been observed in other (non-HSP) transcriptionally active genes.
Right: Circos plot summarizing cis- and trans- intergenic interactions tested within and between different categories of genes. Depicted is the interactome of 10 min HS cells. Strikingly, intergenic interactions have been detected only between Hsf1-regulated genes, as genes regulated by alternative thermal stress responsive factors Msn2 and Msn4 show no detectable interactions in 10 min HS cells.
Genome-wide Organization of HSP Genes and Identification of Molecular Determinants Underlying the Formation of Transcription Factories
Participants: Linda S. Rubio, Vickky Pandit, Raji Meduri, Suman Mohajan
Collaborators: David Pincus (The University of Chicago), Dan Capurso and Yijun Ruan (The Jackson Laboratory for Genomic Medicine)
In mammalian cells, it has been observed that certain types of genes – e.g., those involved in erythroid differentiation, immunoglobulin production, or response to the cytokine TNF-α – cluster together when they are transcriptionally activated into so-called transcription factories. Exactly how and why they do this is unknown. Recent work from our laboratory has revealed that heat-shock responsive genes in budding yeast regulated by the conserved activator Hsf1 likewise coalesce into prominent intranuclear foci upon their transcriptional activation. Such coalescence is rapid, robust yet evanescent, and involves physical interactions between both chromosomally linked and unlinked HSP genes. It is also absolutely dependent on Hsf1 and active transcription (RNA Polymerase II). To extend our understanding of this phenomenon, we are mapping HSP gene interactions genome-wide and identifying the DNA sequences and protein factors that drive Hsf1-regulated genes into coalesced intranuclear foci in response to thermal and other proteotoxic stresses (e.g., ethanol). To do so, we are employing a combination of biochemistry, yeast genetics, 3C, Hi-C, ChIA-PET and fluorescence microscopy.
Chowdhary, S., Kainth, A.S., Pincus, D. and Gross, D.S. 2019. Heat Shock Factor 1 Drives Intergenic Association of Its Target Gene Loci Upon Heat Shock. Cell Reports 26: 18-28.
Genes regulated by Hsf1 intricately fold upon their activation and preferentially interact, coalescing into transcriptionally active foci. In acutely heat-shocked cells, physical interactions take place between Hsf1-regulated HSP genes located throughout the genome. Here are depicted HSP genes (colored pretzels with yellow spheres) residing on the left and right arms of Chr. XII (green ribbon). Such interactions are highly specific, as they exclude neighboring genes regulated by heterologous activators (brown pretzel with red sphere), and are remarkably robust, as they can circumvent the physical barrier imposed by the nucleolus (condensed chromatin domain, upper right).
Role of Mediator in the Transcriptional Regulation and 3D Genomic Organization of Hsf1 Target Genes
Participants: Amol S. Kainth, Vickky Pandit
Mediator is an evolutionarily conserved coactivator complex essential for RNA polymerase II transcription. We have recently evaluated the role of this coactivator in Hsf1-driven transcription and found that it is rapidly and robustly recruited to the UAS/promoter regions of HSP genes in response to heat shock. Mediator occupancy peaks within 2.5 min of exposure to stress, and begins to dissipate shortly thereafter. Interestingly, Hsf1 uses both its N- and C-terminal activation domains to recruit Mediator, engaging in physical and functional interactions with the Med15 Tail module subunit. Using the ‘Anchor Away’ technique to conditionally deplete select subunits within Mediator and its reversibly associating Cdk8-Kinase module (CKM), we have additionally found that Mediator’s Tail module is highly dynamic and that a subcomplex consisting of Med2, Med3 and Med15 can be independently recruited to the UAS regions of Hsf1-activated genes. In addition, and contrary to current models, we have observed that Hsf1 can recruit the CKM independently of core Mediator, and that core Mediator has a role in regulating post-initiation events. Our results therefore suggest that yeast Mediator is not monolithic but potentially has a dynamic complexity heretofore unappreciated. Multiple species, including CKM-Mediator, the 21-subunit core complex, the Med2-Med3-Med15 Tail Triad, and the four-subunit CKM can be independently recruited by activated Hsf1 to its target genes. We are currently exploring the role that Mediator, and in particular its Tail Triad, might play in the intergenic coalescence of HSP genes that takes place upon heat shock.
Anandhakumar J., Moustafa Y.W., Chowdhary S., Kainth A.S. and Gross D.S. 2016. Evidence for multiple Mediator complexes in yeast independently recruited by activated Heat Shock Factor. Mol. Cell. Biol. 36: 1943-1960.
Left: Existence of multiple Mediator complexes in vivo. Those marked with an asterisk (*) have been detected at upstream regulatory regions of heat shock-induced HSP genes.
Genetic and Epigenetic Determinants of Heat Shock Factor 1 Occupancy
Participants: Jayamani Anandhakumar and Alexander Erkine
Collaborators: David Pincus, Pratt Thiru (Whitehead Institute) and Michael Guertin (University of Virginia)
The heat shock transcriptional response is a universal response of organisms to thermal, chemical and oxidative stress. In eukaryotes from yeast to human, proteotoxic conditions activate Heat Shock Factor 1 (Hsf1), which is responsible for the transcriptional induction of genes that encode molecular chaperones and other cytoprotective heat shock proteins (HSPs). Such induction is usually transient as Hsf1 is subject to negative feedback regulation by molecular chaperones, particularly Hsp70 and Hsp90. Our earlier work has suggested that the ability of Hsf1 to bind and remodel chromatin is critical to its biological function in the budding yeast Saccharomyces cerevisiae. In this project our goal is to gain deeper insight into the biology of yeast Hsf1 through mapping its genome-wide occupancy under basal, acutely inducing and chronically inducing conditions, as well as through a determination of the role played by the pre-set chromatin landscape in fostering Hsf1 binding and subsequent, heat shock-dependent chromatin remodeling.
Pincus, D ., Anandhakumar, J., Thiru, P., Guertin, M.J., Erkine, A.M. and Gross, D.S. 2018. Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome. Mol. Biol. Cell 29: 3168-3182.
Left: Hsf1 ChIP-seq reveals differential basal and heat-shock-inducible binding across the Hsf1 regulon. Top, Normalized ChIP signal at 43 core loci occupied under all conditions tested: non-heat shock (NHS), 5 min HS and 120 min HS. Bottom, Normalized ChIP signal at 31 loci occupied only following heat shock. A key distinction between the core and inducibly occupied loci is the presence of accessible, nucleosome-depleted chromatin at the core loci conducive to basal Hsf1 occupancy.
Recent Publications of the Gross Lab
Ethanol stress induces transient restructuring of the yeast genome yet stable formation of Hsf1 transcriptional condensates. Rubio et al (posted on BioRxiv) – September 2023
Work principally of PhD student Linda S. Rubio revealed that transcription factors have functions beyond regulating the expression of their target genes as different stimuli in the budding yeast S. cerevisiae drive distinct transcription, topologic, and phase-separation phenomena dependent on the same transcription factor, Heat Shock Factor 1 (Hsf1).
Thermal stress (heat shock) induces the formation of transient Hsf1 condensates while ethanol stress induces formation of persistent Hsf1 condensates.
Dynamic coalescence of yeast HSP genes bypasses the requirement for actin. Rubio & Gross, Genetics – April 2023
Work of PhD student Linda S. Rubio demonstrated that nuclear actin, which has been implicated in dynamic chromatin rearrangements in yeast and other eukaryotes, plays little or no role in driving 3D genome restructuring of Hsf1-regulated genes in thermally stressed cells.
Inhibition of actin dynamics using either drug or genetic perturbation does not prevent the heat shock-induced interaction between HSP genes.
Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response. Chowdhary et al, Molecular Cell – November 2022 (Collaboration with David Pincus’s Lab, University of Chicago)
Work principally of former PhD student and postdoc Surabhi Chowdhary demonstrated that the transcription factor Hsf1, together with Pol II and the coactivator Mediator, form dynamic transcriptional condensates in cells exposed to acute thermal stress. These condensates drive the repositioning of Heat Shock Response genes that culminates in their coalescence within the condensates.
Phase-separation antagonists potently inhibit transcription and broadly increase nucleosome density. Meduri et al, J. Biol. Chem. – August 2022
Work principally of former postdoc Raji Meduri demonstrated that the aliphatic di-alcohols 1,6- and 2,5-hexanediol (HD), commonly used to study biomolecular condensates in living cells, abrogate transcription of both Pol II and Pol III genes at elevated temperatures (39°C). They do so by globally increasing nucleosome density.
Hexanediols (1,6- or 2,5-HD) in combination with acute heat shock (39°C; HS) strongly suppress Pol II transcription.
Notable Publications of the Gross Lab
Chowdhary, S., Kainth, A.S., Paracha, S., Gross, D.S. and Pincus, D. 2022. Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response. Mol. Cell 82: 4189-4400.
Meduri, R., Rubio, L.S., Mohajan, S. and Gross, D.S. 2022. Phase-separation antagonists potently inhibit transcription and broadly increase nucleosome density. J. Biol. Chem. 298: 102365
Kainth A.S., Chowdhary S., Pincus, D. and Gross D.S. 2021. Primordial Super-Enhancers: Heat Shock-Induced Chromatin Organization. Trends Cell Biol. 31: 801-813
Chowdhary, S., Kainth, A.S. and Gross, D.S. 2020. Chromosome conformation capture that detects novel cis- and trans-interactions in budding yeast. Methods 170: 4-16.
- Chowdhary, S., Kainth, A.S., Pincus, D. and Gross, D.S. 2019. Heat Shock Factor 1 drives intergenic association of its target gene loci upon heat shock. Cell Reports 26: 18-28.
- Pincus, D., Anandhakumar, J., Thiru, P., Guertin, M.J., Erkine, A.M. and Gross, D.S. 2018. Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome. Mol. Biol. Cell 29: 3168-3182.
- Chowdhary, S., Kainth, A.S. and Gross, D.S. 2017. Heat Shock Protein genes undergo dynamic alteration in their three-dimensional structure and genome organization in response to thermal stress. Mol. Cell. Biol. 37: e00292-17, 1-22.
- Anandhakumar, J., Moustafa, Y.W., Chowdhary, S., Kainth, A.S. and Gross, D.S. 2016. Evidence for multiple Mediator complexes in yeast independently recruited by activated Heat Shock Factor. Mol. Cell. Biol. 36: 1943-1960.
- Zhang, H., Gao, L., Anandhakumar, J. and Gross, D.S. 2014. Uncoupling transcription from histone covalent modification. PLoS Genetics 10: e1004202.
• A comment on this paper (“New & Noteworthy”) appeared on the homepage of the Saccharomyces Genome Database (www.yeastgenome.org) on 1 May 2014.
• Selected by Abcam as one of the top epigenetics articles in 2014.
• Featured on the Epigenetics Blog, EpiBeat July 2014.
- Kim, S. and Gross, D.S. 2013. Mediator recruitment to heat shock genes requires dual Hsf1 activation domains and Mediator Tail subunits Med15 and Med16. J. Biol. Chem. 288: 12197-12213.
- Kremer, S.B., Kim, S., Jeon, J.O., Moustafa, Y.W., Chen, A., Zhao, J. and Gross, D.S. 2012. Role of Mediator in regulating Pol II elongation and nucleosome displacement in Saccharomyces cerevisiae. Genetics 191: 95-106.
· Selected as an F1000 Prime article by Faculty of 1000.
- Kim, S., Balakrishnan, S.K. and Gross, D.S. 2011. p53 interacts with RNA polymerase II through its core domain and impairs Pol II processivity in vivo. PLoS ONE 6: e22183.
- Kremer, S.B. and Gross, D.S. 2009. SAGA and Rpd3 chromatin modification complexes dynamically regulate heat shock gene structure and expression. J. Biol. Chem. 284: 32914-32931.
- Gao, L. and Gross, D.S. 2008. Sir2 silences gene transcription by targeting the transition between RNA polymerase II initiation and elongation. Mol. Cell. Biol. 28: 3979-3994.
· Selected as an F1000 Prime article by Faculty of 1000.
- Balakrishnan, S.K. and Gross, D.S. 2008. The tumor suppressor p53 associates with gene coding regions and co-traverses with elongating RNA polymerase II in an in vivo model. Oncogene 27: 2661-2672.
- Singh, H., Erkine, A.M., Kremer, S.B., Duttweiler, H.M., Davis, D.A., Iqbal, J., Gross, R.R. and Gross, D.S. 2006. A functional module of yeast Mediator that governs the dynamic range of heat shock gene expression. Genetics 172: 2169-2184.
- Zhao, J., Herrera-Diaz, J. and Gross, D.S. 2005. Domain-wide displacement of histones by activated heat shock factor occurs independently of Swi/Snf and is not correlated with RNA polymerase II density. Mol. Cell. Biol. 25: 8985-8999.
- Pirrotta, V. and Gross, D. S. 2005. Epigenetic silencing mechanisms in budding yeast and fruitfly: Different paths, same destinations. Mol. Cell 18: 395-398.
- Sekinger, E. A. and Gross, D. S. 2001. Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105: 403-414.
· Featured in News & Comment, Trends in Genetics 17: 381 (2001).
· Selected as an F1000 Prime article by Faculty of 1000.
- Venturi, C. B., Erkine, A.M., and Gross, D.S. 2000. Cell cycle-dependent binding of yeast heat shock factor to nucleosomes. Mol. Cell. Biol. 20: 6435-6448.
- Sekinger, E. A. and Gross, D.S. 1999. SIR repression of a yeast heat shock gene: UAS and TATA footprints persist within heterochromatin. EMBO J. 18: 7041-7055.
- Erkine, A.M., Magrogan, S.F., Sekinger, E. A. and Gross, D.S. 1999. Cooperative binding of heat shock factor to the yeast HSP82 promoter in vivo and in vitro. Mol. Cell. Biol. 19: 1627-1639.
- Erkine, A.M., Adams, C.C., Diken, T., and Gross, D.S. 1996. Heat shock factor gains access to the yeast HSC82 promoter independently of other sequence-specific factors and antagonizes nucleosomal repression of basal and induced transcription. Mol. Cell. Biol. 16: 7004-7017.
- Gross, D.S., Adams, C.C., Lee, S., and Stentz, B. 1993. A critical role for heat shock transcription factor in establishing a nucleosome-free region over the TATA-initiation site of the yeast HSP82 heat shock gene. EMBO J. 13: 3931-3945.
- Lee, S. and Gross, D.S. 1993. Conditional silencing: The HMRE mating-type silencer exerts a rapidly reversible position effect on the yeast HSP82 heat shock gene. Mol. Cell. Biol. 13: 727-738.
- Adams, C.C. and Gross, D.S. 1991. The yeast heat shock response is induced by conversion of cells to spheroplasts and by potent transcriptional inhibitors. J. Bacteriology 173: 7429-7435.
- Gross, D.S., English, K.E., Collins, K.W., and Lee, S. 1990. Genomic footprinting of the yeast HSP82 promoter reveals marked distortion of the DNA helix and constitutive occupancy of heat shock and TATA elements. J. Mol. Biol. 216: 611-631.
- Gross, D.S. and Garrard, W.T. 1988. Nuclease hypersensitive sites in chromatin. Ann. Rev. Biochem. 57: 159-197.
A position is potentially available for a Postdoctoral Fellow. To inquire about opportunities, contact David Gross at firstname.lastname@example.org.
Graduate students interested in conducting research in the Gross Lab should contact David Gross at email@example.com.
Undergraduate Research Assistants
A position is potentially available for an Undergraduate Research Assistant. To inquire about opportunities, contact David Gross at firstname.lastname@example.org.
LSU Health Shreveport
Department of Biochemistry and Microbiology
1501 Kings Hwy
Shreveport, LA 71103