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Research Article

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

Judhajeet Ray, Paul R. Munn, Anniina Vihervaara, James J. Lewis, Abdullah Ozer, Charles G. Danko, and View ORCID ProfileJohn T. Lis
PNAS September 24, 2019 116 (39) 19431-19439; first published September 10, 2019 https://doi.org/10.1073/pnas.1901244116
Judhajeet Ray
aDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
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Paul R. Munn
bBaker Institute for Animal Health, Cornell University, Ithaca, NY 14853
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Anniina Vihervaara
aDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
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James J. Lewis
bBaker Institute for Animal Health, Cornell University, Ithaca, NY 14853
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Abdullah Ozer
aDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
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  • For correspondence: ao223@cornell.edu cgd24@cornell.edu jtl10@cornell.edu
Charles G. Danko
bBaker Institute for Animal Health, Cornell University, Ithaca, NY 14853
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  • For correspondence: ao223@cornell.edu cgd24@cornell.edu jtl10@cornell.edu
John T. Lis
aDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
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  • ORCID record for John T. Lis
  • For correspondence: ao223@cornell.edu cgd24@cornell.edu jtl10@cornell.edu
  1. Contributed by John T. Lis, August 9, 2019 (sent for review January 23, 2019; reviewed by Robert E. Kingston, Roger D. Kornberg, and Bing Ren)

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Significance

Dramatic and rapid changes in transcription take place upon heat shock (HS), where thousands of genes have been shown to be immediately up- or down-regulated in metazoans. The role of large-scale chromatin conformation and changes in long-range interactions between distal regulatory elements and HS-regulated promoters remains unclear. Our study shows that topologically associating domains and compartment structures remain remarkably unchanged upon acute HS in human and Drosophila, while only modest changes of distal regulatory interactions are observed in human cells. These results suggest that the global chromatin structure required for the HS response is preestablished across metazoans in order to drive transcriptional changes in HS responsive genes.

Abstract

Heat shock (HS) initiates rapid, extensive, and evolutionarily conserved changes in transcription that are accompanied by chromatin decondensation and nucleosome loss at HS loci. Here we have employed in situ Hi-C to determine how heat stress affects long-range chromatin conformation in human and Drosophila cells. We found that compartments and topologically associating domains (TADs) remain unchanged by an acute HS. Knockdown of Heat Shock Factor 1 (HSF1), the master transcriptional regulator of the HS response, identified HSF1-dependent genes and revealed that up-regulation is often mediated by distal HSF1 bound enhancers. HSF1-dependent genes were usually found in the same TAD as the nearest HSF1 binding site. Although most interactions between HSF1 binding sites and target promoters were established in the nonheat shock (NHS) condition, a subset increased contact frequency following HS. Integrating information about HSF1 binding strength, RNA polymerase abundance at the HSF1 bound sites (putative enhancers), and contact frequency with a target promoter accurately predicted which up-regulated genes were direct targets of HSF1 during HS. Our results suggest that the chromatin conformation necessary for a robust HS response is preestablished in NHS cells of diverse metazoan species.

  • heat shock
  • Hi-C
  • gene regulation
  • HSF1
  • TADs

Footnotes

  • ↵1J.R. and P.R.M. contributed equally to this work.

  • ↵2To whom correspondence may be addressed. Email: ao223{at}cornell.edu, cgd24{at}cornell.edu, or jtl10{at}cornell.edu.
  • Author contributions: J.R., A.O., C.G.D., and J.T.L. designed research; J.R., P.R.M., A.V., A.O., and C.G.D. performed research; A.V. contributed new reagents/analytic tools; P.R.M., A.V., J.J.L., A.O., and C.G.D. analyzed data; and J.R., P.R.M., C.G.D., and J.T.L. wrote the paper.

  • Reviewers: R.E.K., Massachusetts General Hospital and Harvard Medical School; R.D.K., Stanford University School of Medicine; and B.R., Ludwig Institute for Cancer Research.

  • The authors declare no conflict of interest.

  • Data deposition: The Hi-C data have been deposited at the Gene Expression Omnibus (GEO) database, (accession no. GSE130778). Custom code and example data have been deposited in GitHub, https://github.com/Danko-Lab/HS_transcription_regulation. The Hi-C contact caller program has been deposited in GitHub, https://github.com/Danko-Lab/Hi-C_contact_caller (version: 88efbbf).

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1901244116/-/DCSupplemental.

Published under the PNAS license.

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Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock
Judhajeet Ray, Paul R. Munn, Anniina Vihervaara, James J. Lewis, Abdullah Ozer, Charles G. Danko, John T. Lis
Proceedings of the National Academy of Sciences Sep 2019, 116 (39) 19431-19439; DOI: 10.1073/pnas.1901244116

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Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock
Judhajeet Ray, Paul R. Munn, Anniina Vihervaara, James J. Lewis, Abdullah Ozer, Charles G. Danko, John T. Lis
Proceedings of the National Academy of Sciences Sep 2019, 116 (39) 19431-19439; DOI: 10.1073/pnas.1901244116
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