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Genome Res. 2019 Jan;29(1):18-28. doi: 10.1101/gr.238527.118. Epub 2018 Dec 6.

Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock.

Author information

1
Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.
2
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.
3
Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), E-08003 Barcelona, Spain.
4
CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), E-08003 Barcelona, Spain.
5
Universitat Pompeu Fabra, 08003 Barcelona, Spain.
#
Contributed equally

Abstract

Nuclear architecture is decisive for the assembly of transcriptional responses. However, how chromosome organization is dynamically modulated to permit rapid and transient transcriptional changes in response to environmental challenges remains unclear. Here we show that hyperosmotic stress disrupts different levels of chromosome organization, ranging from A/B compartment changes to reduction in the number and insulation of topologically associating domains (TADs). Concomitantly, transcription is greatly affected, TAD borders weaken, and RNA Polymerase II runs off from hundreds of transcription end sites. Stress alters the binding profiles of architectural proteins, which explains the disappearance of local chromatin organization. These processes are dynamic, and cells rapidly reconstitute their default chromatin conformation after stress removal, uncovering an intrinsic organization. Transcription is not required for local chromatin reorganization, while compartment recovery is partially transcription-dependent. Thus, nuclear organization in mammalian cells can be rapidly modulated by environmental changes in a reversible manner.

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