Recoding in the Brain

Art by Evelyn Jiang.

The human brain is constantly recoding itself. Adenosine-to-inosine (A-to-I) editing, a form of RNA modification, occurs at more than one hundred million sites in the human transcriptome, diversifying RNA sequences of the human brain.

In a recent paper published in Cell Reports, researchers at Icahn School of Medicine at Mount Sinai and the Yale School of Medicine investigated the spatiotemporal and genetic regulation of A-to-I editing over the course of human brain development. Their work catalogs A-to-I editing sites throughout human brain maturation, enhancing current understandings of neurodevelopment and underlying mechanisms of neurological diseases. “RNA editing is dysregulated in neurodevelopmental disorders,” said Winston Cuddleston, a PhD candidate at the Icahn School of Medicine and lead researcher of the study. “We are trying to get a better understanding of which RNA editing sites are dynamically regulated across brain development to realize which cellular and molecular processes are being affected.”

The Science of RNA Editing

According to the central dogma of molecular biology, coined by biophysicist Francis Crick, the expression of protein-coding genes involves the flow of genetic information from DNA to RNA to protein. A gene’s DNA is copied into RNA through transcription, and that RNA specifies an amino acid sequence for protein synthesis in the translation process. 

In eukaryotes, primary RNA transcripts undergo diverse post-transcriptional modifications, resulting in mature RNA molecules prior to protein production. These modifications diversify the transcriptome, the collection of an organism’s RNA transcripts. 

A-to-I editing is a post-transcriptional modification involving adenosine conversion to inosine nucleosides. This conversion process is catalyzed by a family of enzymes called adenosine deaminase acting on RNA (ADAR) and occurs most prominently in the central nervous system (CNS). These modifications affect neuronal genes, including those involved in synaptic transmission and signaling. 

In protein-coding regions, A-to-I editing can result in amino acid substitutions at locations known as recoding sites. These recoding sites are necessary for normal neurodevelopment, given their involvement in modulating calcium permeability, desensitization recovery rates, and cytoskeletal organization at excitatory synapses, alongside other functions. 

Investigation of A-to-I Sites in the Brain

Millions of individual A-to-I editing modifications have been found in humans—many in the brain. Nevertheless, according to this study’s senior author Michael Breen, assistant professor of psychiatry, genetics, and genomic sciences at Mount Sinai, only a small subset of these modifications appears to be functional. “Those sites that are functional have precise temporal patterns across time. Their editing efficiency changes throughout age and development in the brain,” Breen said. 

Breen and colleagues took a systematic look at A-to-I editing sites across prenatal and postnatal stages of human brain maturation. The researchers collected RNA sequencing data from brain samples of the dorsolateral prefrontal cortex (DLPFC), cerebrum, and cerebellum. They also analyzed RNA-sequencing data from in vitro models of neuronal maturation, postmortem cortical samples from late stages of aging, and murine and non-human primate models of brain development. In doing so, the researchers collected brain RNA sequencing data covering the human lifespan.

“RNA editing is dynamically regulated in the brain during aging, and this is a unique property of RNA editing in the brain compared to other tissues in the body,” Cuddleston said. In their paper, Breen, Cuddleston, and colleagues provide an atlas of A-to-I sites that are spatiotemporally and genetically regulated throughout brain maturation while uncovering key features of RNA editing throughout neurodevelopment. In particular, A-to-I editing is enriched in repetitive sequences known as Alu elements. Using an Alu editing index (AEI) to quantify modification levels, Breen and fellow researchers observed that global Alu editing steadily increases across all stages of brain development and neuronal maturation. This editing peaks around thirty to fifty-nine years of age, while advanced aging stages do not exhibit dynamic regulation. 

The researchers identified thousands of editing sites that are temporally regulated and increase in editing levels throughout neurodevelopment. The majority exist in the three-prime untranslated regions (3′ UTRs) of genes critical for neurodevelopment. The minority of spatiotemporally regulated editing sites exist within protein-coding regions, and thirty-seven RNA-recoding sites appear to change in editing levels across maturation. 

The researchers also describe trends in hyper-editing. As opposed to A-to-I editing at individual adenosine nucleosides, hyper-editing refers to modifying many adjacent adenosines along an extended region. The results indicate that hyper-editing is enriched in advanced stages of aging with the function of stabilizing RNA secondary structures. 

A-to-I Editing in Neurodevelopmental Disorders 

Editing rates increase globally throughout brain development. “Global increase is dynamic in different neurological diseases, so it could be looked at as a predictor of brain health,” Breen said. The researchers asked whether sites displaying increased editing throughout brain development are affected in neurodevelopmental disorders. Their results suggest that A-to-I sites disrupted in postmortem brain tissue from individuals with schizophrenia and autism spectrum disorder are temporally regulated, exhibiting an increase in editing levels across maturation. “Knowing what we think these sites do in typical brain development, [i.e.,] modulating the ability of micro-RNAs to regulate host gene expression, and that these sites are disrupted in neurodevelopmental diseases gives an immediate avenue towards trying to understand what these sites might be doing in these disorders,” Breen said.

Recoding sites where A-to-I editing results in amino acid substitutions provide further insight into neurodevelopmental diseases. “A handful of recoding sites have been described as dynamically regulated in Alzheimer’s, schizophrenia, and other neurological disorders,” Breen said. “We know that these sites are important for synaptic transmission, and their editing efficiencies are altered in these different diseased states.”

Additionally, hyper-editing data enhances the current understanding of the aging brain. Only a handful of prior studies investigate RNA hyper-editing, and none consider the developmental regulation of hyper-editing in the brain. Breen and fellow researchers discovered that hyper-editing increases in the aging brain and appears to affect transcript stability rather than directly regulating gene expression. Considering all study datasets, the normalized hyper-editing signal steadily rises across brain development periods and peaks into advanced aging stages. “While site-selective editing peaks in terms of its rate of change in mid-fetal development, hyper-editing continues to accumulate all the way into advanced aging,” Cuddleston said. “This is really important for aging research.” RNA hyper-editing may provide insight into Alzheimer’s disease, for instance, which Cuddleston aims to investigate in the future. 

The Prospects of RNA Biology

In Cell Reports, Breen and colleagues provide an atlas of spatiotemporally and genetically regulated A-to-I sites in the brain throughout human neurodevelopment while unearthing key features of RNA editing throughout the lifespan. These findings not only improve current understandings of human brain development at the RNA level but also provide an avenue for learning more about the foundations of neurodevelopmental disorders. “We know very little about RNA modifications and what those might mean for disease pathology,” Breen said. “We are just starting to paint that picture.”

It is through understanding such diseases at the neurobiological level that progress can be made toward treatment development. “Understanding which RNA editing events are functionally relevant for disease is how we are going to get closer to therapeutics that we can use in the clinic,” Cuddleston said. 
With thousands of temporally regulated RNA editing sites, the brain is a fascinating organ of continual change. How is your brain recoding itself?