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      miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner

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          Abstract

          The circular RNA (circRNA) Cdr1as is conserved across mammals and highly expressed in neurons, where it directly interacts with microRNA miR-7. However, the biological function of this interaction is unknown. Here, using primary cortical murine neurons, we demonstrate that stimulating neurons by sustained depolarization rapidly induces two-fold transcriptional upregulation of Cdr1as and strong post-transcriptional stabilization of miR-7. Cdr1as loss causes doubling of glutamate release from stimulated synapses and increased frequency and duration of local neuronal bursts. Moreover, the periodicity of neuronal networks increases, and synchronicity is impaired. Strikingly, these effects are reverted by sustained expression of miR-7, which also clears Cdr1as molecules from neuronal projections. Consistently, without Cdr1as, transcriptomic changes caused by miR-7 overexpression are stronger (including miR-7-targets downregulation) and enriched in secretion/synaptic plasticity pathways. Altogether, our results suggest that in cortical neurons Cdr1as buffers miR-7 activity to control glutamatergic excitatory transmission and neuronal connectivity important for long-lasting synaptic adaptations.

          Synopsis

          In mouse cortical neurons, miR-7 regulates glutamate release, controlled by the buffering action of Cdr1as. These molecules together govern glutamatergic transmission and neuronal connectivity, influencing synaptic adaptations at transcriptional and neuronal activity levels.

          • Neuronal depolarization transcriptionally induces Cdr1as and post-transcriptionally stabilizes miR-7

          • Cdr1as-KO neurons show chronically elevated neuronal activity, higher asynchrony and oscillation, increased pre-synaptic glutamate release, and inhibition of synaptic adaptation.

          • Cdr1as:miR-7 interaction exerts a synergetic gene regulation of the neuronal transcriptome, compared to their individual mutations. Additionally, miR-7 up-regulation is sufficient to restore local and network neural activity and glutamate secretion, but it depends on Cdr1as expression.

          Abstract

          In mouse cortical neurons, miR-7 regulates glutamate release, controlled by the buffering action of Cdr1as. These molecules together govern glutamatergic transmission and neuronal connectivity, influencing synaptic adaptations at transcriptional and neuronal activity levels.

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          Most cited references36

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          A Threshold Selection Method from Gray-Level Histograms

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            Circular RNAs are a large class of animal RNAs with regulatory potency.

            Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
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              Natural RNA circles function as efficient microRNA sponges.

              MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more than 70 selectively conserved miRNA target sites, and it is highly and widely associated with Argonaute (AGO) proteins in a miR-7-dependent manner. Although the circRNA is completely resistant to miRNA-mediated target destabilization, it strongly suppresses miR-7 activity, resulting in increased levels of miR-7 targets. In the mouse brain, we observe overlapping co-expression of ciRS-7 and miR-7, particularly in neocortical and hippocampal neurons, suggesting a high degree of endogenous interaction. We further show that the testis-specific circRNA, sex-determining region Y (Sry), serves as a miR-138 sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA.
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                Author and article information

                Contributors
                rajewsky@mdc-berlin.de
                Journal
                EMBO Rep
                EMBO Rep
                EMBO Reports
                Nature Publishing Group UK (London )
                1469-221X
                1469-3178
                3 June 2024
                3 June 2024
                July 2024
                : 25
                : 7
                : 3008-3039
                Affiliations
                [1 ]Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, ( https://ror.org/04p5ggc03) Hannoversche Str. 28, 10115 Berlin, Germany
                [2 ]Light Microscopy Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, ( https://ror.org/04p5ggc03) Hannoversche Str. 28, 10115 Berlin, Germany
                [3 ]Helmholtz Imaging, Max-Delbrück-Center for Molecular Medicine, Berlin, ( https://ror.org/04p5ggc03) Germany Hannoversche Str. 28, 10115 Berlin, Germany
                [4 ]Helmholtz AI, Helmholtz Zentrum München, ( https://ror.org/00cfam450) Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
                [5 ]GRID grid.413454.3, ISNI 0000 0001 1958 0162, Department of Non-Coding RNAs, Institute of Bioorganic Chemistry, , Polish Academy of Sciences, ; Noskowskiego 12/14, 61-704 Poznan, Poland
                Author information
                http://orcid.org/0000-0003-1783-5533
                http://orcid.org/0000-0001-8357-0073
                http://orcid.org/0000-0002-3971-3070
                http://orcid.org/0000-0002-6358-2576
                http://orcid.org/0000-0002-4785-4332
                Article
                168
                10.1038/s44319-024-00168-9
                11239925
                38831125
                e6da4297-61df-404d-a936-7b4fedc047dd
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

                History
                : 4 January 2024
                : 12 April 2024
                : 14 May 2024
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft (DFG);
                Award ID: Gottfried Wilhelm Leibniz Prize
                Award ID: DFG EXC2049
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100017270, NeuroCure Exzellenzcluster (NeuroCure Cluster of Excellence);
                Funded by: FundRef http://dx.doi.org/10.13039/100010447, Deutsches Zentrum für Herz-Kreislaufforschung (DZHK);
                Award ID: 81X2100155
                Funded by: EU ITN - circular RNA Biology Training Network
                Award ID: circRTrain (721890)
                Award Recipient :
                Funded by: Helmholtz Association’s Initiative and Networking Fund
                Funded by: Polish National Agency for Academic Exchange
                Award ID: PPN/PPO/2019/1/00035/U/0001
                Award Recipient :
                Funded by: National Science Centre
                Award ID: 2018/30/E/NZ3/00624
                Award Recipient :
                Categories
                Article
                Custom metadata
                © European Molecular Biology Organization 2024

                Molecular biology
                circrna,mirna,neuronal activity,cdr1as,mir-7,neuroscience,rna biology
                Molecular biology
                circrna, mirna, neuronal activity, cdr1as, mir-7, neuroscience, rna biology

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