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Verheyden NA, Klostermann M, Brüggemann M, Steede H, Scholz A, Amr S, Lichtenthaeler C, Münch C, Schmid T, Zarnack K, Krueger A. A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match. Nucleic Acids Res 2024; 52:8515-8533. [PMID: 38783381 PMCID: PMC11317165 DOI: 10.1093/nar/gkae416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3' untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules.
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Affiliation(s)
- Nikita A Verheyden
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Hanna M Steede
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
| | - Anica Scholz
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Shady Amr
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Chiara Lichtenthaeler
- Institute of Molecular Medicine, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Andreas Krueger
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
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Gao Y, Zhu Y, Sun Q, Chen D. Ribosome-associated protein quality control: Implications for neurodegenerative diseases and therapeutic potential. Sci Bull (Beijing) 2024; 69:1165-1169. [PMID: 38278708 DOI: 10.1016/j.scib.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Affiliation(s)
- Yajie Gao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China; Southwest United Graduate School, Kunming 650500, China.
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3
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Li Z, Mao K, Liu L, Xu S, Zeng M, Fu Y, Huang J, Li T, Gao G, Teng ZQ, Sun Q, Chen D, Cheng Y. Nuclear microRNA-mediated transcriptional control determines adult microglial homeostasis and brain function. Cell Rep 2024; 43:113964. [PMID: 38489263 DOI: 10.1016/j.celrep.2024.113964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/01/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Microglia are versatile regulators in brain development and disorders. Emerging evidence links microRNA (miRNA)-mediated regulation to microglial function; however, the exact underlying mechanism remains largely unknown. Here, we uncover the enrichment of miR-137, a neuropsychiatric-disorder-associated miRNA, in the microglial nucleus, and reveal its unexpected nuclear functions in maintaining the microglial global transcriptomic state, phagocytosis, and inflammatory response. Mechanistically, microglial Mir137 deletion increases chromatin accessibility, which contains binding motifs for the microglial master transcription factor Pu.1. Through biochemical and bioinformatics analyses, we propose that miR-137 modulates Pu.1-mediated gene expression by suppressing Pu.1 binding to chromatin. Importantly, we find that increased Pu.1 binding upregulates the target gene Jdp2 (Jun dimerization protein 2) and that knockdown of Jdp2 significantly suppresses the impaired phagocytosis and pro-inflammatory response in Mir137 knockout microglia. Collectively, our study provides evidence supporting the notion that nuclear miR-137 acts as a transcriptional modulator and that this microglia-specific function is essential for maintaining normal adult brain function.
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Affiliation(s)
- Zhu Li
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Kexin Mao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China; Southwest United Graduate School, Kunming 650500, China
| | - Lin Liu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Shengyun Xu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Min Zeng
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yu Fu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Jintao Huang
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Tingting Li
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Guoan Gao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Zhao-Qian Teng
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinmiao Sun
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China; Southwest United Graduate School, Kunming 650500, China.
| | - Ying Cheng
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China; Southwest United Graduate School, Kunming 650500, China.
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4
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Ottens F, Efstathiou S, Hoppe T. Cutting through the stress: RNA decay pathways at the endoplasmic reticulum. Trends Cell Biol 2023:S0962-8924(23)00236-2. [PMID: 38008608 DOI: 10.1016/j.tcb.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, which activates quality control mechanisms to restore ER function and protein homeostasis. Beyond protein quality control, mRNA decay pathways have emerged as potent ER fidelity regulators, but their mechanistic roles in ER quality control and their interrelationships remain incompletely understood. Herein, we review ER-associated RNA decay pathways - including regulated inositol-requiring enzyme 1α (IRE1α)-dependent mRNA decay (RIDD), nonsense-mediated mRNA decay (NMD), and Argonaute-dependent RNA silencing - in ER homeostasis, and highlight the intricate coordination of ER-targeted RNA and protein decay mechanisms and their association with antiviral defense.
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Affiliation(s)
- Franziska Ottens
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sotirios Efstathiou
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany.
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