Many people make dubious claims of being endowed with more than the five traditionally recognized senses; their “sixth sense” providing the extrasensory perception needed to converse with spirits and ghosts and predict the future, among other fanciful claims. While there is a lack of any evidence for extrasensory powers and paranormal activity, robust studies have suggested that epigenetic modifying enzymes have an additional sense that allows them to perceive changes to oxygen levels and alter the epigenetic landscape accordingly.
However, don’t run off and spend all your hard-earned cash at a fortune teller, medium, or telepath to find out the details; stick with us here to learn about the two reports from Finish and British research groups that demonstrate how two lysine-specific demethylase enzymes directly sense oxygen levels and alter histone post-translational modifications. Overall, both sets of authors sought to discover whether histone methylation changes occurring after hypoxia occurred via the hypoxia-inducible factor (HIF) pathway or whether a HIF-independent mode of epigenetic alterations also existed.
In the first of two hypoxia-based epigenetic studies, firmly grounded researchers from the labs of Peppi Koivunen (University of Oulu, Finland) and William G. Kaelin Jr. (Harvard Medical School, Boston, USA) focused on an H3K27 demethylase:
- The team first applied multiplexed mass spectrometric assays in mouse hepatoma cells lacking a functional HIF pathway, where they found that, in response to hypoxia, cells still display alterations to the methylation status of histones
- This finding suggests that hypoxia can act both through the HIF pathway to mediate epigenetic changes and by directly affecting histone modifying enzymes
- The team chose to concentrate on the H3K27me3 histone demethylase KDM6A, as it displays the lowest oxygen affinity of all histone demethylases and given the enticing link between hypoxia and histone H3K27 methylation in the control of cellular differentiation.
- After confirming that hypoxia increases levels of H3K27 methylation in various human cell lines, the authors moved on to study C2C12 murine myoblasts, in which hypoxia inhibits differentiation into multinucleated myotubes
- The loss of KDM6A in this system prevents the demethylation of H3K27 and blocks cellular differentiation in a comparable manner to hypoxia
- Restoring H3K27 methylation homeostasis by inhibition of the reciprocal histone methyltransferase EZH2 in hypoxic cells reverses these effects
- Of note, the biochemical studies by the authors also suggested that at least one H3K4 and one H3K9 histone demethylase can also function as oxygen sensors, creating further intrigue to this sensorial barrage of epigenetic data!
Overall, the authors confirmed that oxygen, and not spirits, poltergeists, and others from the beyond, can influence cell fate by directly affecting histone modifying enzymes.
In the second related study from the always skeptical team at the Sonia Rocha lab (University of Liverpool/University of Dundee, UK), the authors concentrate on a different demethylase:
- The authors first noted that hypoxia-induced alterations to the H3K4me3 and H3K36me3 modifications in human fibroblasts occur at specific genomic locations before transcriptional events and before the stabilization of HIF1a, suggesting independence from the HIF pathway
- Their histone analysis employed acid extraction of histones and quantitative immunofluorescence as well as ChIP-Seq
- These analyses confirmed the direct impact of hypoxia on histone alterations by providing proof that these changes occurred independently of HIF through siRNA-mediated inhibition of HIF1b and selective inhibition of the von Hippel-Lindau protein
- The team then focused on a predicted H3K4me3 demethylase, KDM5A
- They discovered that the loss of KDM5A via siRNA-mediated downregulation mimics hypoxia-induced cellular responses, such as the increased levels of H3K4me3 at the promoters of hypoxia-responsive genes
In summary, the authors did not find any telepathic link to chromatin movements or other spooky goings-on; instead, their findings helped to confirm that histone-modifying enzymes can directly sense oxygen levels to alter gene expression profiles.
Interestingly, phylogenetic sequence analysis conducted within these studies supports the evolution of a direct oxygen-sensing histone demethylase pathway before the HIF pathway. Additionally, the range of epigenetic changes observed under hypoxia also “foretells” the existence of additional epigenetic modifiers with an added perception for changing oxygen levels, such as those that influence methylation at H3K9 and H3K36.
For more information on this extra-sensory epigenetic extravaganza, see the full studies from Chakraborty and colleagues (Science, March 2019) and Batie and colleagues (Science, March 2019) as well as this excellent Perspective piece!