RNA Circles In Your Brain: Noise or a New Class of Genetic Regulators?

In high school biology, you were most likely taught the central dogma of molecular biology; that is, how genetic information flows within your cells. This dogma is often summarized as follows: DNA is transcribed into a linear piece of RNA that provides a template to create proteins, which then act as the workhorses of your cells. However, we often don’t use the word dogma in science unless we are about to contradict it. This “dogma” has been rewritten many times beginning with the discovery of RNA-based genomes that are reverse transcribed into DNA, and other more recent discoveries of catalytic RNA and non-coding RNAs that do not encode any proteins but perform important cellular functions themselves. The authors of this study tackle another fascinating question that again shakes up what we think we understand about RNA and this central dogma: can RNA exist in other shapes besides its normal linear form, and what might these different shapes be doing in our brains?

Are circular RNAs just byproducts of a less common chemical reaction, or do they perform a specific function?

Cellular RNAs do in fact exist as both the canonical linear form, as well as a circular form. Standard linear messenger RNAs, which would normally go on to encode proteins, contain distinct 5’ and 3’ termini and are spliced according to normal rules; however, circular RNAs (circRNAs) are spliced abnormally to produce stable circles. A big debate remains in the field: are these circRNAs just byproducts of a less common chemical reaction or are they produced for some specific cellular function? A collaborative team of researchers from the Berlin Institute for Medical Systems Biology and the Max Planck Institute for Brain Research in Germany set out to address this debate. Their first set of experiments led to an intriguing observation (especially for us neuroscientists): the abundance of these circRNAs was much higher in the brains of rodents than in any other tissue type that they analyzed. Furthermore, evolutionary conservation is often a strong indicator of functionality in biology, so the authors studied how well conserved these circRNAs are from organism to organism. Using bioinformatics, they indeed found that the specific DNA sequences that led to the creation of circRNAs are in fact highly conserved among vertebrates, hinting at important functionality.

Why might these circRNAs be enriched in brain tissue relative to other tissue? This question leads us to the heart of the story. Using high resolution sequencing methods, the authors found that the brain-expressed circRNAs were predominately derived from genes, whose proteins would normally function at synapses, which are the sites of communication between neurons. Furthermore, using techniques to probe the localization of specific circRNAs, they found that many of these circRNAs themselves localized to these same synaptic regions.

When the authors delved deeper and looked at the developing brain, they also identified a cluster of circRNAs that dramatically changed their expression patterns during a critical time window in which synapses begin to form mature connections within the brain. The ability to regulate and vary these synaptic connections throughout life is fundamental to how we learn and respond to experiences. Along these lines, the researchers used a chemical trick to induce their cultured neurons to mimic experience-dependent changes in their connectivity (a state called homeostatic plasticity), and found that after induction of this plasticity, specific circRNAs were upregulated in both the neuron cell body and the dendritic shafts where synaptic connections are formed. Taken together, the authors identified a family of RNAs that form stable circular structures, do not encode any proteins, and exist in the right time and place to play a role in regulating brain development.

This paper, while far from a complete story, nonetheless opens the door for many further studies into what these strange RNA forms are doing in the brain. The authors have presented a great resource for neuroscientists to probe more mechanistically into the functions of specific circRNAs during brain development and synaptogenesis. A major step forward provided by this study was the first unambiguous demonstration of the circular nature of these RNA species, which they accomplished by taking advantage of state of the art long-read sequencing technologies. While this paper still fails to demonstrate any functional data, many ideas have been hypothesized as to how these circRNAs may regulate gene expression. The authors have provided evidence of tissue specificity, developmental regulation, evolutionary conservation, and stimulus-evoked expression of many brain specific circRNAs. The brain, arguably our most complex organ, most likely requires complex layers of gene regulatory mechanisms to produce its plastic nature, and this paper provides compelling evidence to follow up on these circRNAs as important players in these processes.