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Szakats S, McAtamney A, Wilson MJ. Identification of novel microRNAs in the embryonic mouse brain using deep sequencing. Mol Cell Biochem 2024; 479:297-311. [PMID: 37059894 PMCID: PMC10890980 DOI: 10.1007/s11010-023-04730-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/04/2023] [Indexed: 04/16/2023]
Abstract
Many advances in small RNA-seq technology and bioinformatics pipelines have been made recently, permitting the discovery of novel miRNAs in the embryonic day 15.5 (E15.5) mouse brain. We aimed to improve miRNA discovery in this tissue to expand our knowledge of the regulatory networks that underpin normal neurodevelopment, find new candidates for neurodevelopmental disorder aetiology, and deepen our understanding of non-coding RNA evolution. A high-quality small RNA-seq dataset of 458 M reads was generated. An unbiased miRNA discovery pipeline identified fifty putative novel miRNAs, six of which were selected for further validation. A combination of conservation analysis and target functional prediction was used to determine the authenticity of novel miRNA candidates. These findings demonstrate that miRNAs remain to be discovered, particularly if they have the features of other small RNA species.
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Affiliation(s)
- Susanna Szakats
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Alice McAtamney
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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Parkins EV, Brager DH, Rymer JK, Burwinkel JM, Rojas D, Tiwari D, Hu YC, Gross C. Mir324 knockout regulates the structure of dendritic spines and impairs hippocampal long-term potentiation. Sci Rep 2023; 13:21919. [PMID: 38082035 PMCID: PMC10713680 DOI: 10.1038/s41598-023-49134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
MicroRNAs are an emerging class of synaptic regulators. These small noncoding RNAs post-transcriptionally regulate gene expression, thereby altering neuronal pathways and shaping cell-to-cell communication. Their ability to rapidly alter gene expression and target multiple pathways makes them interesting candidates in the study of synaptic plasticity. Here, we demonstrate that the proconvulsive microRNA miR-324-5p regulates excitatory synapse structure and function in the hippocampus of mice. Both Mir324 knockout (KO) and miR-324-5p antagomir treatment significantly reduce dendritic spine density in the hippocampal CA1 subregion, and Mir324 KO, but not miR-324-5p antagomir treatment, shift dendritic spine morphology, reducing the proportion of thin, "unstable" spines. Western blot and quantitative Real-Time PCR revealed changes in protein and mRNA levels for potassium channels, cytoskeletal components, and synaptic markers, including MAP2 and Kv4.2, which are important for long-term potentiation (LTP). In line with these findings, slice electrophysiology revealed that LTP is severely impaired in Mir324 KO mice, while neurotransmitter release probability remains unchanged. Overall, this study demonstrates that miR-324-5p regulates dendritic spine density, morphology, and plasticity in the hippocampus, potentially via multiple cytoskeletal and synaptic modulators.
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Affiliation(s)
- Emma V Parkins
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, OH, 45229, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Darrin H Brager
- Center for Learning and Memory, Department of Neuroscience, The University of Texas at Austin, Austin, USA
| | - Jeffrey K Rymer
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - John M Burwinkel
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Diego Rojas
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Durgesh Tiwari
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, OH, 45229, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Yueh-Chiang Hu
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Transgenic Animal and Genome Editing Core Facility, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Christina Gross
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, OH, 45229, USA.
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
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Parkins EV, Burwinkel JM, Ranatunga R, Yaser S, Hu YC, Tiwari D, Gross C. Age-Dependent Regulation of Dendritic Spine Density and Protein Expression in Mir324 KO Mice. J Mol Neurosci 2023; 73:818-830. [PMID: 37773316 PMCID: PMC10793736 DOI: 10.1007/s12031-023-02157-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/08/2023] [Indexed: 10/01/2023]
Abstract
Dendritic spines are small, dynamic protrusions along the dendrite that comprise more than 90% of excitatory connections in the brain, making them essential sites for neuronal communication. These synaptic sites change throughout the process of development, reducing in density and shifting morphology as synapses are refined. One important class of dendritic spine regulators is microRNA (miRNA), small-noncoding RNAs that post-transcriptionally regulate gene expression. Several studies suggest that miRNA-324-5p regulates dendritic spine formation. In addition, we have previously shown that miR-324-5p plays a role in seizure and long-term potentiation, both of which involve dendritic spine changes. In this study, we aimed to characterize the role of miRNA-324-5p in developmental spine regulation by assessing the effect of Mir324 knockout (KO) on dendritic spine density and expression of a subset of dendritic proteins at select developmental time points. We show that miR-324-5p expression is developmentally regulated and peaks at 4 weeks of age. We demonstrate that loss of miR-324-5p expression leads to differential changes in both target protein expression and spine density at different time points during development, disrupting the pattern of spine density changes and leading to a premature loss of dendritic spines in KO mice, which is compensated later. Our findings indicate that miR-324-5p plays a role in synaptic refinement across development. Additionally, our data illustrate the importance of context in the study of miRNA, as regulation by and/or of miRNA can vary dramatically across development and in disease.
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Affiliation(s)
- Emma V Parkins
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, OH, 45229, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - John M Burwinkel
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ruvi Ranatunga
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Sarah Yaser
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, OH, 45229, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Yueh-Chiang Hu
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Transgenic Animal and Genome Editing Core Facility, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Durgesh Tiwari
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Christina Gross
- University of Cincinnati Neuroscience Graduate Program, Cincinnati, OH, 45229, USA.
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
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4
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Parkins EV, Burwinkel JM, Ranatunga R, Yaser S, Hu YC, Tiwari D, Gross C. Age-dependent regulation of dendritic spine density and protein expression in Mir324 KO mice. RESEARCH SQUARE 2023:rs.3.rs-3221779. [PMID: 37609225 PMCID: PMC10441466 DOI: 10.21203/rs.3.rs-3221779/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Dendritic spines are small, dynamic protrusions along the dendrite that comprise more than 90% of excitatory connections in the brain, making them essential sites for neuronal communication. These synaptic sites change throughout the process of development, reducing in density and shifting morphology as synapses are refined. One important class of dendritic spine regulators is microRNA (miRNA), small noncoding RNAs that post-transcriptionally regulate gene expression. Several studies suggest that miRNA-324-5p regulates dendritic spine formation. In addition, we have previously shown that miR-324-5p plays a role in seizure and long-term potentiation, both of which involve dendritic spine changes. In this study, we aimed to characterize the role of miRNA-324-5p in developmental spine regulation by assessing the effect of Mir324 knockout (KO) on dendritic spine density and expression of a subset of dendritic proteins at select developmental time points. We show that miR-324-5p expression is developmentally regulated and peaks at four weeks of age. We demonstrate that loss of miR-324-5p expression leads to differential changes in both target protein expression and spine density at different time points during development, disrupting the pattern of spine density changes and leading to a premature loss of dendritic spines in KO mice, which is compensated later. Our findings indicate that miR-324-5p plays a role in synaptic refinement across development. Additionally, our data illustrate the importance of context in the study of miRNA, as regulation by and/or of miRNA can vary dramatically across development and in disease.
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Affiliation(s)
| | | | | | - Sarah Yaser
- Cincinnati Children's Hospital Medical Center
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Kadkhoda S, Hussen BM, Eslami S, Ghafouri-Fard S. A review on the role of miRNA-324 in various diseases. Front Genet 2022; 13:950162. [PMID: 36035118 PMCID: PMC9399342 DOI: 10.3389/fgene.2022.950162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/04/2022] [Indexed: 12/02/2022] Open
Abstract
Recent studies have revealed important functions of several microRNAs (miRNAs) in the pathogenesis of human diseases. miR-324 is an example of miRNAs with crucial impacts on the pathogenesis of a wide range of disorders. Gene ontology studies have indicated possible role of miR-324 in responses of cells to the leukemia inhibitory factor, long-term synaptic potentiation, positive regulation of cytokines production and sensory perception of sound. In human, miR-324 is encoded by MIR324 gene which resides on chromosome 17p13.1. In the current manuscript, we provide a concise review of the role of miR-324 in the pathogenesis of cancers as well as non-cancerous conditions such as aneurysmal subarachnoid hemorrhage, diabetic nephropathy, epilepsy, pulmonary/renal fibrosis, ischemic stroke and ischemia reperfusion injuries. Moreover, we summarize the role of this miRNA as a prognostic marker for malignant disorders.
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Affiliation(s)
- Sepideh Kadkhoda
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Soudeh Ghafouri-Fard,
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