It is essential for living organisms to manage which genes are activated and in which cells at specific times. Modifications in DNA-binding histone proteins are thought to be vital in this regulatory process. Nevertheless, it was previously uncertain whether these modifications actively influence gene expression. Recent studies have demonstrated that specific sites on histones serve as crucial control points, helping prevent unintended activation of genes, including those originating from ancient viral DNA sequences.
For the survival and growth of any organism, cells must carefully manage which genes are turned on and off at different times and places. Recent findings from EMBL Heidelberg’s Noh Group along with collaborators from EMBL Australia reveal significant control sites that oversee this regulatory process, particularly in relation to the behavior of ancient viral sequences in the genome.
The human genome is vast, with each of our cells containing over 6 billion base pairs of DNA. This massive amount of information makes it challenging to locate the specific data needed for particular functions at any given moment. This is where epigenetic signatures come into play.
If we compare the genome to a book, epigenetic marks can be seen as the highlights and notes added to its pages. However, it’s often unclear whether these marks are truly directive – meaning do they tell the cell to “read this” or to “ignore this”? Or are they merely remnants left by someone who read that section before?
This question intrigued Kyung-Min Noh, Group Leader at EMBL Heidelberg, and her team. They focused on a histone protein known as H3.3, which binds tightly to DNA to help form its functional structure.
The H3.3 protein features several sites on its tail (notably K9 and K27) that frequently undergo chemical modifications. It is proposed that these changes serve as epigenetic markers that guide the cell in deciding whether to express certain genes. However, until now, there has been no experimental confirmation that these specific sites act as real control points in directing gene expression.
To test this, the researchers created a mutated version of H3.3 that could not be chemically modified at those locations. Using our book analogy, this mutation resulted in a page that could not be highlighted or annotated, allowing scientists to observe the effects of losing those modifications directly.
Additionally, this system permitted the researchers to choose which specific page would be protected, enabling them to compare the effects of losing marks at each control site.
The findings revealed that mutating these sites in mouse stem cells led to issues with cell differentiation, growth, and survival, and also caused unintended activation of genes throughout the genome. This included genes that should not have been active in stem cells, such as those associated with the immune system.
This indicates that a normal function of these sites is to keep these genes in an inactive or ‘repressed’ state, thereby allowing stem cells to retain their identity. The impacts of these mutations differed between the two control sites examined, highlighting that each serves a unique role in gene regulation.
Further investigation revealed that the regions that were typically silenced but activated when histone sites were mutated are remnants of ancient viruses that have integrated into our genomes.
“These regions are known as endogenous retroviruses (ERVs),” stated Matteo Trovato, a former PhD student in the Noh group and lead author of the study, who is currently a postdoc at IFOM, Italy. “Over evolutionary time, the host’s genome has utilized these regions to perform regulatory functions. For instance, in immune cells, about 30% of enhancers (a specific category of regulatory DNA) are sourced from ERVs.”
The researchers discovered that modifying the K9 site in stem cells resulted in many of these ‘hidden’ enhancers – typically inactive DNA regulatory regions – becoming active.
“Maintaining repression of these unique genomic areas is critical for maintaining the balance of the cell’s gene expression programs,” remarked Noh. “When these cryptic enhancers are activated, it leads to significant alterations in the gene regulatory network, ultimately affecting the identity and functionality of stem cells.”
This research was conducted in collaboration with Chen Davidovich’s group at EMBL Australia, Benjamin Garcia’s laboratory at Washington University in St. Louis, and Judith Zaugg’s team at EMBL Heidelberg. The findings were recently published in the journal Nature Communications.
“This is among the first studies to demonstrate in a mammalian context that these histone residues have a direct role in gene regulation,” said Noh. “Understanding these mechanisms could have significant implications for fields such as developmental biology and disease research, particularly concerning cancers and neurological disorders, where gene regulation is crucial.”
