An RNA:DNA “sandwich” plays a key role in behavioral adaptations arising from emotional experiences

A team of neuroscience researchers at the Medical University of South Carolina reports in Science the discovery of a new genetic regulatory mechanism involved in behavioral adaptations to emotional experiences in a preclinical model. Although such adaptations are crucial for survival, they can become problematic in patients with certain psychiatric disorders. Understanding the genetic changes that lead to maladaptive behaviors may help scientists to develop better RNA therapies to treat brain disorders.

The research team included Makoto Taniguchi, Ph.D., assistant professor in the Department of Neuroscience, Christopher Cowan, Ph.D., professor and chair of the Department of Neuroscience, and Rose Marie Akiki, an M.D. Ph.D. student at MUSC. With funding from the National Institutes of Health and a pilot grant from the South Carolina Clinical & Translational Research Institute, the researchers set out to understand how clinically relevant emotional experiences, including chronic stress and drug use, lead to long-lasting changes in behavior. Ultimately, their findings show that loss of this genetic regulatory mechanism leads to reduced drug seeking and increased resilience to stress in mice.

“By understanding this process, we hope to get better insights into how changes in the brain can lead to maladaptive changes in behavior,” said Cowan. “We could also improve our fundamental understanding of how the brain works and how emotions and emotionally relevant experiences help to shape brain circuits.”

Scientists have long known that what we experience can cause changes in our brain, thereby altering how we behave. But how exactly do those changes occur? Well, it begins with our genes.

“This is a new way of thinking about how genes can be turned on. (…) We could also improve our fundamental understanding of how the brain works and how emotions and emotionally relevant experiences help to shape brain circuits.”

-- Dr. Christopher Cowan

All cells within an individual contain essentially the same genes, but different genes can be turned on at different times. This variability allows our bodies to adapt to a changing environment. Importantly, well over half of the human genome is devoted to producing a specific type of regulatory molecules that help to control when and where critical protein-coding genes are turned on. These regulatory molecules, known as long non-coding RNAs (lncRNAs), have been found to differ in people with depression and substance use disorders.

The MUSC researchers focused on long non-coding enhancer RNA (Inc-eRNA), a specific type of lncRNA that interacts with the regulatory region of target genes. Upon binding to specific genes, Inc-eRNA can form unique structures, known as R-loops, to help to govern those genes.

“We found that neurons, like immune cells, can respond to a stimulus through the formation of an R-loop.”

-- Rose-Marie Akiki

The MUSC team looked at a gene called NPAS4, which is implicated in both stress-induced anhedonia, or lack of joy in activities that were once pleasurable, and drug-induced relapse. Their study provides the first evidence for the role of R-loops in governing behavioral changes induced by emotional experiences.

R-loops can help to turn on specific genes by forming an RNA:DNA “sandwich” in regulatory regions of a target gene. In the case of the NPAS4 gene, R-loops appear to help to bring the enhancer region, which includes instructions for turning on a gene and is located at a distance, together with the main body of the gene, including the important gene promoter region, and this allows the gene to be turned on in response to an experience.

“By bringing the enhancer and promoter together in space and time, R-loops seem to be facilitating their interaction and driving the response to turn on a gene,” said Cowan.

In response to emotional experiences, some people struggle more than others, and this may result in the development of maladaptive behaviors. For example, the death of a loved one is a very difficult experience to process that could lead some individuals to develop depression, while others are able to make peace with their loss. The specific behaviors the researchers analyzed in mice were cocaine seeking and a response to chronic stress, as these are clinically relevant responses to particularly emotional experiences.

When the researchers blocked the formation of R loops in front of the NPAS4 gene in the region of the brain known as the nucleus accumbens, they found that mice did not show a preference for cocaine. When a similar manipulation was performed in the prefrontal cortex, mice did not develop behaviors mimicking stress-induced anhedonia. These findings suggest that lnc-eRNAs, and associated R-loops, at the NPAS4 gene are an important process in the brain by which emotional experiences can produce behaviors associated with substance use or mood disorders.

“You need a change in the genetic basis of how everything is working, what is being transcribed, what is being formed in the cell to form stronger neural circuits that underlie behavior,” said Akiki.

The lnc-eRNA that the researchers focus on is highly conserved among species, which demonstrates the evolutionary relevance of this regulatory molecule. In fact, R-loops have been found in other cell types as well. The formation of R-loops with eRNAs is known to be an important mechanism in the immune system for developing immunity.

“If this really is a general mechanism, we want to see how stable it is and how it gets disrupted in pathological conditions.” 

-- Dr. Makoto Taniguchi

Akiki speculated that R-loops might be involved in the ability of neural circuits to adapt to experience-induced changes, drawing on her knowledge of immunology.

“I didn't think that evolution would favor a different mechanism for neurons,” she said. “We found that neurons, like immune cells, can respond to a stimulus through the formation of an R-loop.”

In the future, the research team wants to understand how ubiquitous this genetic regulatory mechanism is in the brain.

“If this really is a general mechanism, we want to see how stable it is and how it gets disrupted in pathological conditions,” said Taniguchi.

This newly discovered genetic mechanism could contribute to the way we respond to emotionally significant experiences in life. Ultimately, this finding helps to deepen our understanding of how the brain interprets experiences to influence adaptive behavior.

“This is a new way of thinking about how genes can be turned on,” said Cowan.

By developing a deeper understanding of the fundamental genetic processes that lead to behavioral changes, the findings of this paper may potentially inform novel applications of RNA-based therapies for the treatment of psychiatric disorders.

Reference 

Akiki RM, Cornbrooks RG, Magami K, Greige A, Snyder KK, Wood DJ, Herrington MC, Mace P, Blidy K, Koike N, Berto S, Cowan CW, Taniguchi M. A long non-coding eRNA forms R-loops to shape emotional experience-induced behavioral adaptation. Science. 2024, Dec 13; 386 (6727): 1282-1289. doi: 10.1126/science.adp1562. Epub 2024 Dec 12.