Heterochromatin, sometimes known as the “dark side of the genome,” is a poorly studied fraction of DNA that makes up about half of our genetic material. For more than 50 years scientists have puzzled over the genetic material contained in this “dark DNA,” but are now starting to unravel its role in cells. There’s a growing body of evidence showing that its proper functioning is critical for maintaining cells in a healthy state. Heterochromatin contains tens of thousands of units of dangerous DNA, known as transposable elements (TEs). In normal cells, TEs remain silently buried in heterochromatin, but under many pathological conditions, they can wake up and occasionally even “jump” into our regular genetic code.
And if that change benefits a cell? Transposable elements have been co-opted for new purposes through evolutionary history—for instance, the RAG genes in immune cells and the genes required for driving the development of the placenta and mammalian evolution have been derived from TEs.
But TEs may also wreak havoc on our health. Over recent years scientists have linked weakening heterochromatin to aging, premalignancy, cancer, and autoimmune disease. “You can think of heterochromatin as a prison for transposable elements,” said research lead Anjana Rao, PhD, a professor at the La Jolla Institute for Immunology (LJI). “When heterochromatin loses its normal suppressive function, TEs escape and in parallel, the health of cells declines.”
In a newly reported study Rao, together with Geoffrey J. Faulkner, PhD, a professor at the University of Queensland, and colleagues identified a remarkable way that cells keep us safe from TEs gone wild. The researchers found that cells have taken advantage of an entire protein network to repress TE activity and keep themselves healthy. Their research indicated that O-GlcNAc transferase (OGT), an enzyme at the heart of many essential cellular functions, is also a lead choreographer when it comes to suppressing TEs and keeping gene expression running smoothly.
The scientists suggest their findings could help identify new potential therapeutic approaches for cancer. Lead author Rao and colleagues reported on the study in Nature Structural & Molecular Biology, in an article titled, “OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide.”
“Reactivated transposable elements can create a lot of genomic instability,” explained Hugo Sepulveda, PhD, a Pew Latin American Postdoctoral Fellow, former instructor at LJI, and one of the two co-first authors of the new study, together with LJI instructor Xiang Li, PhD. “Even just increased expression of these elements can affect the expression of nearby genes, as we show in our new paper. Abundant expression of transposable elements is a signature of many diseases, including cellular senescence, human aging, autoimmune disorders, and many types of cancers.”
For the new project, the researchers followed up on the fact that OGT interacts with important proteins called TET enzymes, discovered by the Rao Lab in 2009. “O-GlcNAc transferase (OGT) interacts robustly with all three mammalian TET methylcytosine dioxygenases,” they wrote in their paper. TET proteins are part of the complex machinery that makes sure our DNA is correctly modified in our cells and that our cells activate the right transcriptional programs.
TET proteins are involved in the critical cycle of DNA modifications, where they play a role in a process that results in the removal of molecular markers that attach to DNA (an event called DNA demethylation). The most abundant DNA markers, called 5mC and 5hmC, are normally associated with transcriptional silencing and activation, respectively. Researchers have shown that 5mC is associated with genes turned “off” while 5hmC, mediated by TET proteins, is associated with gene expression turned “on.” They further noted in their report, “The three mammalian members of the TET family (TET1, TET2, and TET3) catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and beyond.”
This “on/off” epigenetic system gives our cells the flexibility to respond to environmental changes and health threats. DNA demethylation helps our immune cells spring into action if they detect a threat.
DNA demethylation is normal, but cells also need balance. You can’t have TET proteins activating every gene at the same time. In normal cells, TET protein activity is restricted to the genes that need to be expressed in that particular cell type.
In the new study, the scientists harnessed Oxford Nanopore sequencing technology and other cutting-edge sequencing techniques to discover where OGT comes in. One especially important and new technique that they used is called duet evoC. This multiomics solution enabling the 6-base genome, developed by biomodal, was essential to establish that both 5mC and 5hmC were simultaneously changing at the same sites in the genome. They described this 6-base sequencing technology as “… a base-resolution method that simultaneously detects 5hmC, 5mC, and all four canonical bases in a single sequencing run.”
The researchers found that OGT protects cells by restraining TET activity. This is extremely important for controlling TE expression because it prevents the silencing modification 5mC from being converted to the activating modification 5hmC in heterochromatin.
Without OGT at the helm, TET proteins ramp up DNA demethylation in the wrong places, turning on too many genes at once, including intact TEs normally “buried” in our genetic material. “Thus, OGT, through its catalytic activity and the TET–OGT interaction, restrains TET activity genome-wide, maintaining genome stability by suppressing widespread DNA demethylation and the consequent increase in TE expression,” the investigators stated.
The findings show how the noncoding regions of our genome can turn active when TET functions are altered. The new understanding of the OGT-TET partnership shows that these proteins, their mediated marks, and TE expression can affect our cells in a big way. “We think of these elements as totally ‘silent,’ and therefore completely inert, but the reality is that cells have to make a huge—and constant—investment to keep TEs silent,” said Sepulveda.
This new research may also prove important for future drug development. Scientists have identified numerous genes linked to cancer, but controlling their expression remains a challenge. The new study results suggest we might stop cancer growth through interesting new avenues, such as by restraining TE activity in cancer cells. As the team reported in their paper, “We suggest that OGT protects the genome against TET-mediated DNA demethylation and loss of heterochromatin integrity, preventing the aberrant increase in transposable element expression noted in cancer, autoimmune-inflammatory diseases, cellular senescence, and aging.”
“We want to control that activity, and we may now have an option through OGT and TETs,” said Sepulveda. Rao emphasized that further studies are needed to investigate how OGT controls DNA modifications and TE expression—and how the dysregulation of this mechanism contributes to autoimmune disorders, cancers, and other diseases.