Study maps cerebral cortex genes related to neuron dysfunction

Researchers compared the repertoire of long non-coding RNAs in humans with those of rhesus monkeys, mice, and chickens and noted that these structures played a role in functional specialization throughout evolution.

By Ricardo Muniz  |  Agência FAPESP – Research conducted by Brazilian scientists and published in the journal Molecular Biology and Evolution has identified long noncoding RNAs (lncRNAs) active in the human cerebral cortex and mapped their evolution. The study involved the Butantan Institute and the University of São Paulo’s Institute of Chemistry (IQ-USP) and was supported by FAPESP. 

Long non-coding RNAs are genes that do not translate into functional proteins. The research group aimed to understand when these RNAs emerged during the evolution of the cortex in humans and other species and to identify their role in the complex organization of the brain. This information could help characterize their involvement in neurodevelopmental disorders. Although some characteristics may suggest that lncRNAs are merely transcriptional noise, research has shown that they have regulatory functions and the ability to acquire new functional modalities. Thus, a better understanding of their role may reveal potential therapeutic targets.

Important comparisons

The way brain cells function depends on which sets of genes are activated in each cell type and tissue. The cortex, the region responsible for processing information that gives humans immense cognitive capacity, is affected by neurodevelopmental disorders.

To characterize the evolution of the cortex, the outermost layer of the brain, the group compared the human lncRNA repertoire with those of three other vertebrate species. “Using gene transcription and genome comparison data, we made the first detailed and complete annotation of the genes transcribed in the cortex of humans, rhesus monkeys, mice, and chickens and classified the long non-coding RNAs into four distinct evolutionary groups based on their predicted ages,” explains Sergio Verjovski-Almeida, a researcher at the Cell Cycle Laboratory of the Butantan Institute and a professor at the Department of Biochemistry at IQ-USP.

The oldest lncRNAs are present in humans and chickens and emerged more than 300 million years ago. Those present in humans and mice emerged more than 90 million years ago. The most recent ones appeared over 25 million years ago and are found in humans and rhesus monkeys. The researchers also identified lncRNAs that were not present in the other three species studied and are specific to humans.

The authors systematically evaluated the contribution of lncRNAs, compiling a comprehensive catalog. “We show that they exhibit signatures that suggest they’ve played a role in functional specialization throughout evolution,” they say. “We used comparative transcriptomics and genomics to characterize the evolution of the lncRNA repertoire, and our analyses identified signatures of different evolutionary pathways for lncRNAs over time,” they point out.

Older lncRNAs are preferentially expressed near developmental regulatory genes, while newer lncRNAs are selectively expressed in excitatory neurons – precisely those that are dysregulated in patients with neurodevelopmental disorders, such as autism spectrum disorder (ASD). The results suggest that these structures require further study.

“The analyses showed that the oldest lncRNAs were preferentially expressed in germinative zones, in outer radial glial cells, and in inhibitory GABAergic neurons [which inhibit the activity of other neurons by producing the neurotransmitter GABA] in the cortex. On the other hand, the younger ones showed preferential expression in excitatory glutamatergic neurons of the cortex [which stimulate other neurons by producing glutamate] – and appear to be dysregulated in patients with autism or autism accompanied by epilepsy,” explains Verjovski-Almeida.

Unexplored potential

Understanding how the structures of the cerebral cortex function on a molecular level is fundamental to unraveling the evolution of human cognition and gaining a deeper understanding of how it is impaired by diseases. For this reason, the authors argue that considerable effort has been made over the last decade to identify these changes, but the focus has been on the expression of protein-coding genes. However, it is now necessary to expand these analyses to the non-coding transcriptome, or the set of RNAs that do not give rise to proteins. “This is crucial to improving our understanding of the regulatory modifications of genes that led to the evolution of the human cerebral cortex.”

One challenge is finding the most relevant experimental models and cellular processes and searching for lncRNAs that are key targets in these processes. Another challenge is showing the loss and gain of function in a given cell type or organ when their transcription is repressed or overexpressed.

The work of the group was important because, in recent years, the intensive use of large-scale sequencing to detect gene expression in various organisms has revealed that thousands of lncRNAs represent a specific and diverse class of RNAs. Nevertheless, only a few dozen of these RNAs in humans have had their molecular mechanisms identified and characterized in detail.

In addition to Verjovski-Almeida, the work involved David Morales-Vicente, Ana Tahira, Murilo Amaral, and two of Verjovski-Almeida’s FAPESP-supported students: Daisy Woellner-Santos (19/09404-3) and Maria Gabriela Berzoti-Coelho (20/02976-9).

The article “The Human Developing Cerebral Cortex Is Characterized by an Elevated De Novo Expression of Long Noncoding RNAs in Excitatory Neurons” can be read at academic.oup.com/mbe/article/41/7/msae123/7697981.