Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identify over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1526 and 3308 circRNAs are custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 29% of Parkinson’s and 12% of Alzheimer’s disease-associated genes produced validated circRNAs. circDNAJC6, which is transcribed from a juvenile-onset Parkinson’s gene, is already dysregulated during prodromal, onset stages of common Parkinson’s disease neuropathology. Globally, addiction-associated genes preferentially produce circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA-regulated synaptic specialization in neuropsychiatric diseases.
Discussion
Human brain cells custom tailor thousands of circRNAs to fit their cell identity. For many loci, which lacked diversity in linear mRNA expression, the corresponding “companion” circRNAs were cell-type specific. Dopamine and pyramidal neurons prominently expressed circRNAs from synaptic genes and non-neuronal cells prominently produced circRNAs from loci involved in cell cycle regulation.
The sheer number and diversity of circRNAs add a new class of components to the growing inventory of non-coding RNAs actively expressed in the human brain disease18,51,52, including enhancer RNAs18, microRNAs33, and long-non-coding RNAs51. Indeed, there is reason to hypothesize that this expanding regulatory network of non-coding RNAs may be a major contributor to the exceptional diversity and performance of human brain cells that cannot be explained by the surprisingly small number of protein-coding genes in the human genome which are similar in humans and worms52. The fact that circRNAs are predominantly expressed from synapse loci in human dopamine and pyramidal neurons raises the possibility that they encode as yet unknow important functions in synaptic functions of the human neuronal networks controlling quintessential human experiences: fine motor movements, motivation, reward, and higher cortical functions. This expands on a postulated role for circRNAs in synaptosomes4,5 and synaptic plasticity4 in animals. What could that function be? It could be regulation of transcription consistent with the literature2,4,25,53,54. Alternatively, circRNAs—similar to some linear RNAs— might be targeted to the synapse as local regulatory switches that control the translation or assembly of highly specialized synaptic machinery for each type of neuron55. Their circular conformation may confer functional advantages (e.g., longer half-life) or suit transport along axons.
Importantly, 61% of all synaptic circRNAs were linked to brain disorders. Synaptic dysfunction—synaptopathy—may be one of the earliest defects in these neurodegenerative and neuropsychiatric diseases56,57,58,59,60,61. For example, in both toxic and genetic animal models of PD, synaptic plasticity is disrupted during the early phases of dopaminergic dysfunction, much earlier than nigral cell death and the clinical manifestation of motor features57. Disease-linked circRNAs expression showed, in part, evidence of cell type bias: Addiction-associated genes prominently express circRNAs in dopamine neurons, autism genes express circRNAs predominantly in pyramidal neurons, and interestingly, PD GWAS-associated loci express circRNAs highly in non-neuronal cells as well as in neurons. Based on these and prior data4,5,8,11,62, we hypothesize that circRNAs may serve as finely tuned, special-purpose RNA vehicles for the assembly of cell type-specific synapses and that their dysregulation may contribute to synaptopathies. The mechanisms controlling the biogenesis of cell type-specific circRNAs could involve subsets of RNA binding proteins (e.g. refs. 27,28,29 and Supplementary Fig. 4). Much more work will be required to fully elucidate the kinetics and relation of circular and cognate linear RNA biogenesis, the involved regulators, and to reveal how this complex RNA machinery specifies neuron identity and synapses.
More generally, this study provides a unique catalog of circRNAs in two major types of human brain neurons that will be generally useful for decoding genome function in neuropsychiatric disease and for advancing the burgeoning field of RNA medicines and diagnostics63,64,65.
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