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Epigenetics Chromatin. 2016 Oct 26;9:46. doi: 10.1186/s13072-016-0086-0. eCollection 2016.

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3.

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Department of Molecular Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
Department of Bioinformatics (BiGCaT), Maastricht University Medical Centre, Maastricht, The Netherlands.
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University Medical Centre, Maastricht, The Netherlands.
Maastricht Radiation Oncology (MaastRO) Laboratory, Maastricht University Medical Centre, Maastricht, The Netherlands.
Princess Margaret Cancer Centre and Campbell Family Institute for Cancer Research, University Health Network, Toronto, ON Canada.
Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.
Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, ON Canada.
Department of Radiation Oncology, University of Toronto, Toronto, ON Canada.
Contributed equally



Trimethylation at histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) controls gene activity during development and differentiation. Whether H3K4me3 and H3K27me3 changes dynamically in response to altered microenvironmental conditions, including low-oxygen conditions commonly present in solid tumors, is relatively unknown. Demethylation of H3K4me3 and H3K27me3 is mediated by oxygen and 2-oxoglutarate dioxygenases enzymes, suggesting that oxygen deprivation (hypoxia) may influence histone trimethylation. Using the MCF7 breast epithelial adenocarcinoma cell model, we have determined the relationship between epigenomic and transcriptomic reprogramming as a function of fluctuating oxygen tension.


We find that in MCF7, H3K4me3 and H3K27me3 marks rapidly increase at specific locations throughout the genome and are largely reversed upon reoxygenation. Whereas dynamic changes are relatively highest for H3K27me3 marking under hypoxic conditions, H3K4me3 occupation is identified as the defining epigenetic marker of transcriptional control. In agreement with the global increase of H3K27 trimethylation, we provide direct evidence that the histone H3K27me3 demethylase KDM6B/JMJD3 is inactivated by limited oxygen. In situ immunohistochemical analysis confirms a marked rise of histone trimethylation in hypoxic tumor areas. Acquisition of H3K27me3 at H3K4me3-marked loci results in a striking increase in "bivalent" epigenetic marking. Hypoxia-induced bivalency substantially overlaps with embryonal stem cell-associated genic bivalency and is retained at numerous loci upon reoxygenation. Transcriptional activity is selectively and progressively dampened at bivalently marked loci upon repeated exposure to hypoxia, indicating that this subset of genes uniquely maintains the potential for epigenetic regulation by KDM activity.


These data suggest that dynamic regulation of the epigenetic state within the tumor environment may have important consequences for tumor plasticity and biology.


Bivalent marking; Cancer stemness; Chromatin immunoprecipitation; Deep sequencing; H3K27me3; H3K4me3; Histone demethylase; Hypoxia; KDM; Reoxygenation; Tumor plasticity

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