Shuttling Gene Activating Proteins Through Packed Histones Treats Neurodegenerative Disease

Cells can switch off genes by tightly packaging DNA around proteins called histones. However, scientists at St. Jude Children's Research Hospital discovered that under certain conditions, this packaging acts more like molasses than a solid, allowing a specially designed chemical adaptor to shuttle gene-activating proteins through the packaging to the silenced gene inside.

Further, the researchers showed that this process reactivates the gene frataxin, which is abnormally silenced in the neurodegenerative disease Friedreich's ataxia. The study, published today in Nature Cell Biology, challenges a longstanding assumption that histone chemical modifications operate in a simple 'on' or 'off' binary manner.

Researchers have long reported that histones with 'off' modifications can exist at genes that are actively expressed; those examples were often treated as oddities or exceptions to the rule. We are proposing that the barriers can be present, but if the right gene-activating protein is recruited into that environment, the cell treats it more like a road bump than a stop sign."

Aseem Ansari, Corresponding Author, St. Jude Department of Chemical Biology & Therapeutics 

BRD4 Acts as a Condensate Stepping-Stone

In Friedreich's ataxia, the frataxin gene gains hundreds of extra copies of short repeat DNA sequences. These sequences attract machinery that places chemical modifications on histones called methylation marks. A protein called HP1 reads these marks and packs these sections into compact viscous compartments called condensates which aberrantly silence the gene. Ansari's team sought to disrupt this process and free the frataxin gene using their synthetic gene regulator called SynGR1. This molecule binds the short repeat DNA sequences and recruits the gene-activating protein BRD4 to the site. However, they discovered a paradox: the gene was activating, but the methylation marks signaling the repressive "off" state were strengthening.

"To our surprise, the repressive methylation marks and HP1 levels actually increased rather than decreased as expression levels went up," Ansari said. "This made no sense initially, but after years of follow-up work, it became clear that the marks truly were not going away."

The researchers found that BRD4 could enter the repressive HP1 condensate environment and bring gene expression machinery, such as RNA polymerase II, along with it. "We found it is possible to retain repressive methylation marks and still achieve gene expression if there are other factors assisting the polymerase along the way," Ansari said. "With our SynGR1 system, we have provided what amounts to stepping-stones-places where the polymerase can move from one BRD4 molecule to another and continue progressing within this otherwise hostile environment."

The findings suggest that HP1 condensates could be targeted to reactivate genes that have been wrongly switched off, such as in Friedreich's ataxia, or suppress genes that are abnormally active, such as in Huntington's disease. The study also offers a note of caution in making functional statements regarding histone modifications.

"We currently understand perhaps 20 histone modifications - or think we do. Once you begin combining them, the number of possible states becomes enormous, and the complexity becomes overwhelming," Ansari said. "Even with detailed maps, it remains difficult to predict what it will actually take to overcome repression at a given site. Our main takeaway message for this phenomenon is that context really matters."