Quantitative imaging of chromatin decompaction in living cells

Molecular Biology of the Cell
Elisa DultzKarsten Weis

Abstract

Chromatin organization is highly dynamic and regulates transcription. Upon transcriptional activation, chromatin is remodeled and referred to as "open," but quantitative and dynamic data of this decompaction process are lacking. Here, we have developed a quantitative high resolution-microscopy assay in living yeast cells to visualize and quantify chromatin dynamics using the GAL7-10-1 locus as a model system. Upon transcriptional activation of these three clustered genes, we detect an increase of the mean distance across this locus by >100 nm. This decompaction is linked to active transcription but is not sensitive to the histone deacetylase inhibitor trichostatin A or to deletion of the histone acetyl transferase Gcn5. In contrast, the deletion of SNF2 (encoding the ATPase of the SWI/SNF chromatin remodeling complex) or the deactivation of the histone chaperone complex FACT lead to a strongly reduced decompaction without significant effects on transcriptional induction in FACT mutants. Our findings are consistent with nucleosome remodeling and eviction activities being major contributors to chromatin reorganization during transcription but also suggest that transcription can occur in the absence of detectable decompaction.

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Citations

Aug 23, 2018·Molecular Biology of the Cell·Anne de Bruyn KopsChristine Guthrie
Nov 23, 2019·The Journal of Cell Biology·Carina Patrizia DerrerElisa Dultz
Apr 22, 2020·Nature Nanotechnology·Lucien E WeissYoav Shechtman
Jul 8, 2020·Nature Reviews. Endocrinology·Sean L McGee, Mark Hargreaves
Jul 8, 2019·Trends in Endocrinology and Metabolism : TEM·Sean L McGee, Mark Hargreaves
Apr 6, 2021·Current Opinion in Plant Biology·Célia Baroux
Aug 20, 2021·Critical Reviews in Biotechnology·Vikram Singh, Mukesh Jain
Sep 2, 2021·Biophysics Reviews·Ruth NussinovHyunbum Jang

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Methods Mentioned

BETA
acetylation
histone acetylation
PCR
smFISH
immunoprecipitation
specific
superresolution microscopy
dissection

Software Mentioned

VisiVIEW
Diatrack
smFISH
FIJI ImageJ
multcomp
NIS Elements
lme4
MATLAB
IMP
R

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