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Lee H, Roh SH. Cryo-EM structures of human DICER dicing a pre-miRNA substrate. FEBS J 2024; 291:3072-3079. [PMID: 38151772 DOI: 10.1111/febs.17048] [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: 10/12/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023]
Abstract
Dicer, a multi-domain ribonuclease III (RNase III) protein, is crucial for gene regulation via RNA interference. It processes hairpin-like precursors into microRNAs (miRNAs) and long double-stranded RNAs (dsRNAs) into small interfering RNAs (siRNAs). During the "dicing" process, the miRNA or siRNA substrate is stably anchored and cleaved by Dicer's RNase III domain. Although numerous studies have investigated long dsRNA cleavage by Dicer, the specific mechanism by which human Dicer (hDICER) processes pre-miRNA remains unelucidated. This review introduces the recently revealed hDICER structure bound to pre-miRNA uncovered through cryo-electron microscopy and compares it with previous reports describing Dicer. The domain-wise movements of the helicase and dsRNA-binding domain (dsRBD) and specific residues involved in substrate sequence recognition have been identified. During RNA substrate binding, the hDICER apical domains and dsRBD recognize the pre-miRNA termini and cleavage site, respectively. Residue rearrangements in positively charged pockets within the apical domain influence substrate recognition and cleavage site determination. The specific interactions between dsRBD positively charged residues and nucleotide bases near the cleavage site emphasize the significance of cis-acting elements in the hDICER processing mechanism. These findings provide valuable insights for understanding hDICER-related diseases.
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Affiliation(s)
- Hansol Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Soung-Hun Roh
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
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2
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Frédérick PM, Jannot G, Banville I, Simard M. Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals. Nucleic Acids Res 2024; 52:6253-6268. [PMID: 38613392 PMCID: PMC11194074 DOI: 10.1093/nar/gkae272] [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: 08/18/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
MicroRNAs (miRNAs) are essential regulators of several biological processes. They are loaded onto Argonaute (AGO) proteins to achieve their repressive function, forming the microRNA-Induced Silencing Complex known as miRISC. While several AGO proteins are expressed in plants and animals, it is still unclear why specific AGOs are strictly binding miRNAs. Here, we identified the co-chaperone DNJ-12 as a new interactor of ALG-1, one of the two major miRNA-specific AGOs in Caenorhabditis elegans. DNJ-12 does not interact with ALG-2, the other major miRNA-specific AGO, and PRG-1 and RDE-1, two AGOs involved in other small RNA pathways, making it a specific actor in ALG-1-dependent miRNA-mediated gene silencing. The loss of DNJ-12 causes developmental defects associated with defective miRNA function. Using the Auxin Inducible Degron system, a powerful tool to acutely degrade proteins in specific tissues, we show that DNJ-12 depletion hampers ALG-1 interaction with HSP70, a chaperone required for miRISC loading in vitro. Moreover, DNJ-12 depletion leads to the decrease of several miRNAs and prevents their loading onto ALG-1. This study uncovers the importance of a co-chaperone for the miRNA function in vivo and provides insights to explain how different small RNAs associate with specific AGO in animals.
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Affiliation(s)
- Pierre-Marc Frédérick
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Guillaume Jannot
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Isabelle Banville
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Martin J Simard
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
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3
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Tsai YC, Kuo TN, Lin RC, Tsai HL, Chao YY, Lee PR, Su PJ, Wang CY. MicroRNA‑155‑5p inhibits trophoblast cell proliferation and invasion by disrupting centrosomal function. Mol Med Rep 2024; 29:85. [PMID: 38551159 PMCID: PMC10995658 DOI: 10.3892/mmr.2024.13209] [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: 11/15/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024] Open
Abstract
Recurrent miscarriage is used to refer to more than three pregnancy failures before 20 weeks of gestation. Defective trophoblast cell growth and invasion are frequently observed in recurrent miscarriage. Several microRNAs (miRs), including miR‑155‑5p, are aberrantly upregulated in recurrent miscarriage; however, the underlying molecular mechanisms remain unclear. The centrosome orchestrates microtubule networks and coordinates cell cycle progression. In addition, it is a base for primary cilia, which are antenna‑like organelles that coordinate signaling during development and growth. Thus, deficiencies in centrosomal functions can lead to several disease, such as breast cancer and microcephaly. In the present study, the signaling cascades were analyzed by western blotting, and the centrosome and primary cilia were observed and analyzed by immunofluorescence staining. The results showed that overexpression of miR‑155‑5p induced centrosome amplification and blocked primary cilia formation in trophoblast cells. Notably, centrosome amplification inhibited trophoblast cell growth by upregulating apoptotic cleaved‑caspase 3 and cleaved‑poly (ADP‑ribose) polymerase in miR‑155‑5p‑overexpressing trophoblast cells. In addition, overexpression of miR‑155‑5p inhibited primary cilia formation, thereby inhibiting epithelial‑mesenchymal transition and trophoblast cell invasion. All phenotypes could be rescued when cells were co‑transfected with the miR‑155‑5p inhibitor, thus supporting the role of miR‑155‑5p in centrosomal functions. It was also found that miR‑155‑5p activated autophagy, whereas disruption of autophagy via the depletion of autophagy‑related 16‑like 1 alleviated miR‑155‑5p‑induced apoptosis and restored trophoblast cell invasion. In conclusion, the present study indicated a novel role of miR‑55‑5p in mediating centrosomal function in recurrent miscarriage.
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Affiliation(s)
- Yung-Chieh Tsai
- Department of Obstetrics and Gynecology, Chi-Mei Medical Center, Tainan 710, Taiwan, R.O.C
- Department of Sport Management, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan, R.O.C
| | - Tian-Ni Kuo
- Department of Obstetrics and Gynecology, Chi-Mei Medical Center, Tainan 710, Taiwan, R.O.C
| | - Ruei-Ci Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
| | - Hui-Ling Tsai
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
| | - Yu-Ying Chao
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
| | - Pei-Rong Lee
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
| | - Ping-Jui Su
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
| | - Chia-Yih Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
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Huang P, Yu H, Asad M, Liao J, Lin S, Pang S, Chu X, Yang G. Functional characteristics of Dicer genes in Plutella xylostella. PEST MANAGEMENT SCIENCE 2024; 80:2109-2119. [PMID: 38133081 DOI: 10.1002/ps.7945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/21/2023] [Accepted: 12/22/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Dicer is an endonuclease that belongs to the RNase III family and can specifically recognize and cleave double-stranded RNA (dsRNA). In most insects, there are two Dicer genes, Dicer-1 (Dcr-1) and Dicer-2 (Dcr-2), which are involved in the micro-RNA and small-interfering RNA pathways in many species, respectively. The function of Dicer in Plutella xylostella remains unknown. RESULTS The full-length open reading frames of P. xylostella Dicer-1 (PxDcr-1) and Dicer-2 (PxDcr-2) were cloned and sequenced. Dcr-1 and Dcr-2 proteins shared similar structural domains with the Dicer-Partner Binding Domain (Dicer-PBD) and the double-strand RNA binding domain (dsRBD) present only in Dcr-1. The phylogenetic trees showed that lepidopteran Dcr-1s or Dcr-2s clustered in one branch, with PxDcr-1 in the basal position and PxDcr-2 closest to Plodia interpunctella Dicer. Two homozygous knockout lines, ΔPxDcr-1 and ΔPxDcr-2, were obtained by using the CRISPR-Cas9 technique. The ΔPxDcr-1 strain exhibited a high mortality rate, a low eclosion rate, a low egg-laying rate, a low hatching rate, and a shriveled ovariole without mature eggs. The ΔPxDcr-2 strain showed no significant difference from the wild-type in terms of survival, development and reproduction, but the RNA interference (RNAi) efficiency caused by dsRNA was significantly reduced. CONCLUSION These findings demonstrate the involvement of PxDcr-1 in the development and reproduction of P. xylostella, specifically in the formation of ovarioles and eggs, and PxDcr-2 is indispensable for RNAi. These findings shed light on the function of Dcr-1 and Dcr-2 in Lepidoptera. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Pengrong Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Yu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Asad
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianying Liao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sujie Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Senbo Pang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuemei Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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5
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Le CT, Nguyen TD, Nguyen TA. Two-motif model illuminates DICER cleavage preferences. Nucleic Acids Res 2024; 52:1860-1877. [PMID: 38167721 PMCID: PMC10899750 DOI: 10.1093/nar/gkad1186] [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: 08/11/2023] [Revised: 11/25/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
In humans, DICER is a key regulator of gene expression through its production of miRNAs and siRNAs by processing miRNA precursors (pre-miRNAs), short-hairpin RNAs (shRNAs), and long double-stranded RNAs (dsRNAs). To advance our understanding of this process, we employed high-throughput dicing assays using various shRNA variants and both wild-type and mutant DICER. Our analysis revealed that DICER predominantly cleaves shRNAs at two positions, specifically at 21 (DC21) and 22 (DC22) nucleotides from their 5'-end. Our investigation identified two different motifs, mWCU and YCR, that determine whether DICER cleaves at DC21 or DC22, depending on their locations in shRNAs/pre-miRNAs. These motifs can work together or independently to determine the cleavage sites of DICER. Furthermore, our findings indicate that dsRNA-binding domain (dsRBD) of DICER enhances its cleavage, and mWCU strengthens the interaction between dsRBD and RNA, leading to an even greater enhancement of the cleavage. Conversely, YCR functions independently of dsRBD. Our study proposes a two-motif model that sheds light on the intricate regulatory mechanisms involved in gene expression by elucidating how DICER recognizes its substrates, providing valuable insights into this critical biological process.
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Affiliation(s)
- Cong Truc Le
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
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Estevez-Castro CF, Rodrigues MF, Babarit A, Ferreira FV, de Andrade EG, Marois E, Cogni R, Aguiar ERGR, Marques JT, Olmo RP. Neofunctionalization driven by positive selection led to the retention of the loqs2 gene encoding an Aedes specific dsRNA binding protein. BMC Biol 2024; 22:14. [PMID: 38273313 PMCID: PMC10809485 DOI: 10.1186/s12915-024-01821-4] [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: 02/07/2022] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Mosquito borne viruses, such as dengue, Zika, yellow fever and Chikungunya, cause millions of infections every year. These viruses are mostly transmitted by two urban-adapted mosquito species, Aedes aegypti and Aedes albopictus. Although mechanistic understanding remains largely unknown, Aedes mosquitoes may have unique adaptations that lower the impact of viral infection. Recently, we reported the identification of an Aedes specific double-stranded RNA binding protein (dsRBP), named Loqs2, that is involved in the control of infection by dengue and Zika viruses in mosquitoes. Preliminary analyses suggested that the loqs2 gene is a paralog of loquacious (loqs) and r2d2, two co-factors of the RNA interference (RNAi) pathway, a major antiviral mechanism in insects. RESULTS Here we analyzed the origin and evolution of loqs2. Our data suggest that loqs2 originated from two independent duplications of the first double-stranded RNA binding domain of loqs that occurred before the origin of the Aedes Stegomyia subgenus, around 31 million years ago. We show that the loqs2 gene is evolving under relaxed purifying selection at a faster pace than loqs, with evidence of neofunctionalization driven by positive selection. Accordingly, we observed that Loqs2 is localized mainly in the nucleus, different from R2D2 and both isoforms of Loqs that are cytoplasmic. In contrast to r2d2 and loqs, loqs2 expression is stage- and tissue-specific, restricted mostly to reproductive tissues in adult Ae. aegypti and Ae. albopictus. Transgenic mosquitoes engineered to express loqs2 ubiquitously undergo developmental arrest at larval stages that correlates with massive dysregulation of gene expression without major effects on microRNAs or other endogenous small RNAs, classically associated with RNA interference. CONCLUSIONS Our results uncover the peculiar origin and neofunctionalization of loqs2 driven by positive selection. This study shows an example of unique adaptations in Aedes mosquitoes that could ultimately help explain their effectiveness as virus vectors.
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Affiliation(s)
- Carlos F Estevez-Castro
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
- CNRS UPR9022, Inserm U1257, Université de Strasbourg, 67084, Strasbourg, France
| | - Murillo F Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403-5289, USA
| | - Antinéa Babarit
- CNRS UPR9022, Inserm U1257, Université de Strasbourg, 67084, Strasbourg, France
| | - Flávia V Ferreira
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Elisa G de Andrade
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
- CNRS UPR9022, Inserm U1257, Université de Strasbourg, 67084, Strasbourg, France
| | - Eric Marois
- CNRS UPR9022, Inserm U1257, Université de Strasbourg, 67084, Strasbourg, France
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, State University of Santa Cruz, Ilhéus, 45662-900, Brazil
| | - João T Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
- CNRS UPR9022, Inserm U1257, Université de Strasbourg, 67084, Strasbourg, France.
| | - Roenick P Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
- CNRS UPR9022, Inserm U1257, Université de Strasbourg, 67084, Strasbourg, France.
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7
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Bofill-De Ros X, Vang Ørom UA. Recent progress in miRNA biogenesis and decay. RNA Biol 2024; 21:1-8. [PMID: 38031325 PMCID: PMC10761092 DOI: 10.1080/15476286.2023.2288741] [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] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
MicroRNAs are a class of small regulatory RNAs that mediate regulation of protein synthesis by recognizing sequence elements in mRNAs. MicroRNAs are processed through a series of steps starting from transcription and primary processing in the nucleus to precursor processing and mature function in the cytoplasm. It is also in the cytoplasm where levels of mature microRNAs can be modulated through decay mechanisms. Here, we review the recent progress in the lifetime of a microRNA at all steps required for maintaining their homoeostasis. The increasing knowledge about microRNA regulation upholds great promise as therapeutic targets.
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Affiliation(s)
- Xavier Bofill-De Ros
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ulf Andersson Vang Ørom
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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8
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Shang R, Lee S, Senavirathne G, Lai EC. microRNAs in action: biogenesis, function and regulation. Nat Rev Genet 2023; 24:816-833. [PMID: 37380761 PMCID: PMC11087887 DOI: 10.1038/s41576-023-00611-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/30/2023]
Abstract
Ever since microRNAs (miRNAs) were first recognized as an extensive gene family >20 years ago, a broad community of researchers was drawn to investigate the universe of small regulatory RNAs. Although core features of miRNA biogenesis and function were revealed early on, recent years continue to uncover fundamental information on the structural and molecular dynamics of core miRNA machinery, how miRNA substrates and targets are selected from the transcriptome, new avenues for multilevel regulation of miRNA biogenesis and mechanisms for miRNA turnover. Many of these latest insights were enabled by recent technological advances, including massively parallel assays, cryogenic electron microscopy, single-molecule imaging and CRISPR-Cas9 screening. Here, we summarize the current understanding of miRNA biogenesis, function and regulation, and outline challenges to address in the future.
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Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Gayan Senavirathne
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
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9
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Hussen BM, Saleem SJ, Abdullah SR, Mohamadtahr S, Hidayat HJ, Rasul MF, Taheri M, Kiani A. Current landscape of miRNAs and TGF-β signaling in lung cancer progression and therapeutic targets. Mol Cell Probes 2023; 72:101929. [PMID: 37683829 DOI: 10.1016/j.mcp.2023.101929] [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: 08/11/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Lung cancer (LC) is the primary reason for cancer-associated fatalities globally. Due to both tumor-suppressing and tumor-promoting activities, the TGF-β family of growth factors is extremely essential to tumorigenesis. A non-coding single-stranded short RNA called microRNA (miRNA), which is made up of about 22 nt and is encoded by endogenous genes, can control normal and pathological pathways in various kinds of cancer, including LC. Recent research demonstrated that the TGF-β signaling directly can affect the synthesis of miRNAs through suppressor of mothers against decapentaplegic (SMAD)-dependent activity or other unidentified pathways, which could generate allostatic feedback as a result of TGF-β signaling stimulation and ultimately affect the destiny of cancer tissues. In this review, we emphasize the critical functions of miRNAs in lung cancer progression and, more critically, how they affect the TGF-β signaling pathway, and explore the role of both the TGF-β signaling pathway and miRNAs as potential therapeutic targets for improving the treatments of LC patients.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Department of Biomedical Sciences, Cihan University-Erbil, Erbil, Kurdistan Region, 44001, Iraq
| | - Safeen Jasim Saleem
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sayran Mohamadtahr
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Arda Kiani
- Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Lung Research and Developmental Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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10
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [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: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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11
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Ma S, Kotar A, Hall I, Grote S, Rouskin S, Keane SC. Structure of pre-miR-31 reveals an active role in Dicer-TRBP complex processing. Proc Natl Acad Sci U S A 2023; 120:e2300527120. [PMID: 37725636 PMCID: PMC10523476 DOI: 10.1073/pnas.2300527120] [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: 01/11/2023] [Accepted: 08/01/2023] [Indexed: 09/21/2023] Open
Abstract
As an essential posttranscriptional regulator of gene expression, microRNA (miRNA) levels must be strictly maintained. The biogenesis of many miRNAs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers, and interestingly, its biogenesis is not known to be regulated by protein-binding partners. Therefore, the intrinsic structural properties of the precursor element of miR-31 (pre-miR-31) can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of pre-miR-31 to investigate the role of distinct structural elements in regulating processing by the Dicer-TRBP complex. We found that the presence or absence of mismatches within the helical stem does not strongly influence Dicer-TRBP processing of the pre-miRNAs. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by the Dicer-TRBP complex. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influences processing by the Dicer-TRBP complex. Our results enrich our understanding of the active role that RNA structure plays in regulating miRNA biogenesis, which has direct implications for the control of gene expression.
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Affiliation(s)
- Sicong Ma
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
| | - Anita Kotar
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
| | - Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Scott Grote
- Department of Microbiology, Harvard Medical School,Boston, MA02115
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School,Boston, MA02115
| | - Sarah C. Keane
- Biophysics Program, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
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12
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Deng T, Su S, Yuan X, He J, Huang Y, Ma J, Wang J. Structural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers. Nat Commun 2023; 14:5228. [PMID: 37633971 PMCID: PMC10460399 DOI: 10.1038/s41467-023-40919-1] [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: 11/20/2022] [Accepted: 08/16/2023] [Indexed: 08/28/2023] Open
Abstract
Small interference RNAs are the key components of RNA interference, a conserved RNA silencing or viral defense mechanism in many eukaryotes. In Drosophila melanogaster, Dicer-2 (DmDcr-2)-mediated RNAi pathway plays important roles in defending against viral infections and protecting genome integrity. During the maturation of siRNAs, two cofactors can regulate DmDcr-2's functions: Loqs-PD that is required for dsRNA processing, and R2D2 that is essential for the subsequent loading of siRNAs into effector Ago2 to form RISC complexes. However, due to the lack of structural information, it is still unclear whether R2D2 and Loqs-PD affect the functions of DmDcr-2 simultaneously. Here we present several cryo-EM structures of DmDcr-2/R2D2/Loqs-PD complex bound to dsRNAs with various lengths by the Helicase domain. These structures revealed that R2D2 and Loqs-PD can bind to different regions of DmDcr-2 without interfering with each other. Furthermore, the cryo-EM results demonstrate that these complexes can form large oligomers and assemble into fibers. The formation and depolymerization of these oligomers are associated with ATP hydrolysis. These findings provide insights into the structural mechanism of DmDcr-2 and its cofactors during siRNA processing.
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Affiliation(s)
- Ting Deng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Xun Yuan
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinqiu He
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ying Huang
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.
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13
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Kim HJ, Han CW, Jeong MS, Jang SB. Structural study of novel vaccinia virus E3L and dsRNA-dependent protein kinase complex. Biochem Biophys Res Commun 2023; 665:1-9. [PMID: 37146409 DOI: 10.1016/j.bbrc.2023.04.107] [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: 04/10/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
E3L (RNA-binding protein E3) is one of the key IFN resistance genes encoded by VV and consists of 190 amino acids with a highly conserved carboxy-terminal double-stranded RNA-binding domain (dsRBD). PKR (dsRNA-dependent protein kinase) is an IFN-induced protein involved in anti-cell and antiviral activity. PKR inhibits the initiation of translation through alpha subunit of the initiation factor eIF2 (eIF2α) and mediates several transcription factors such as NF-κB, p53 or STATs. Activated PKR also induces apoptosis in vaccinia virus infection. E3L is required for viral IFN resistance and directly binds to PKR to block activation of PKR. In this work, we determined the three-dimensional complex structure of E3L and PKR using cryo-EM and determined the important residues involved in the interaction. In addition, PKR peptide binds to E3L and can increase protein levels of phosphorus-PKR and phosphorus-eIF2α-induced cell apoptosis through upregulation of phosphorus-PKR in HEK293 cells. Taken together, structural insights into E3L and PKR will provide a new optimization and development of vaccinia virus drugs.
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Affiliation(s)
- Hyeon Jin Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Chang Woo Han
- Insitute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Mi Suk Jeong
- Insitute for Plastic Information and Energy Materials and Sustainable Utilization of Photovoltaic Energy Research Center, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan, 46241, Republic of Korea; GJMEDI INC., Republic of Korea.
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea; Insitute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan, 46241, Republic of Korea.
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14
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Szpotkowski K, Wójcik K, Kurzyńska-Kokorniak A. Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques. Comput Struct Biotechnol J 2023; 21:2858-2872. [PMID: 37216015 PMCID: PMC10195699 DOI: 10.1016/j.csbj.2023.04.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Protein-nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge of the biological functions and molecular mechanisms beyond the activity of the macromolecular complexes can be determined from their tertiary structures. Undoubtably, performing structural studies of protein-nucleic acid complexes is challenging, mainly because these types of complexes are often unstable. In addition, their individual components may display extremely different surface charges, causing the complexes to precipitate at higher concentrations used in many structural studies. Due to the variety of protein-nucleic acid complexes and their different biophysical properties, no simple and universal guideline exists that helps scientists chose a method to successfully determine the structure of a specific protein-nucleic acid complex. In this review, we provide a summary of the following experimental methods, which can be applied to study the structures of protein-nucleic acid complexes: X-ray and neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force microscopy (AFM), small angle scattering (SAS) methods, circular dichroism (CD) and infrared (IR) spectroscopy. Each method is discussed regarding its historical context, advancements over the past decades and recent years, and weaknesses and strengths. When a single method does not provide satisfactory data on the selected protein-nucleic acid complex, a combination of several methods should be considered as a hybrid approach; thus, specific structural problems can be solved when studying protein-nucleic acid complexes.
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15
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How does precursor RNA structure influence RNA processing and gene expression? Biosci Rep 2023; 43:232489. [PMID: 36689327 PMCID: PMC9977717 DOI: 10.1042/bsr20220149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/24/2023] Open
Abstract
RNA is a fundamental biomolecule that has many purposes within cells. Due to its single-stranded and flexible nature, RNA naturally folds into complex and dynamic structures. Recent technological and computational advances have produced an explosion of RNA structural data. Many RNA structures have regulatory and functional properties. Studying the structure of nascent RNAs is particularly challenging due to their low abundance and long length, but their structures are important because they can influence RNA processing. Precursor RNA processing is a nexus of pathways that determines mature isoform composition and that controls gene expression. In this review, we examine what is known about human nascent RNA structure and the influence of RNA structure on processing of precursor RNAs. These known structures provide examples of how other nascent RNAs may be structured and show how novel RNA structures may influence RNA processing including splicing and polyadenylation. RNA structures can be targeted therapeutically to treat disease.
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16
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17
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Structure of the human DICER-pre-miRNA complex in a dicing state. Nature 2023; 615:331-338. [PMID: 36813958 DOI: 10.1038/s41586-023-05723-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/14/2022] [Indexed: 02/24/2023]
Abstract
Dicer has a key role in small RNA biogenesis, processing double-stranded RNAs (dsRNAs)1,2. Human DICER (hDICER, also known as DICER1) is specialized for cleaving small hairpin structures such as precursor microRNAs (pre-miRNAs) and has limited activity towards long dsRNAs-unlike its homologues in lower eukaryotes and plants, which cleave long dsRNAs. Although the mechanism by which long dsRNAs are cleaved has been well documented, our understanding of pre-miRNA processing is incomplete because structures of hDICER in a catalytic state are lacking. Here we report the cryo-electron microscopy structure of hDICER bound to pre-miRNA in a dicing state and uncover the structural basis of pre-miRNA processing. hDICER undergoes large conformational changes to attain the active state. The helicase domain becomes flexible, which allows the binding of pre-miRNA to the catalytic valley. The double-stranded RNA-binding domain relocates and anchors pre-miRNA in a specific position through both sequence-independent and sequence-specific recognition of the newly identified 'GYM motif'3. The DICER-specific PAZ helix is also reoriented to accommodate the RNA. Furthermore, our structure identifies a configuration of the 5' end of pre-miRNA inserted into a basic pocket. In this pocket, a group of arginine residues recognize the 5' terminal base (disfavouring guanine) and terminal monophosphate; this explains the specificity of hDICER and how it determines the cleavage site. We identify cancer-associated mutations in the 5' pocket residues that impair miRNA biogenesis. Our study reveals how hDICER recognizes pre-miRNAs with stringent specificity and enables a mechanistic understanding of hDICER-related diseases.
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18
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Komatsu S, Kitai H, Suzuki HI. Network Regulation of microRNA Biogenesis and Target Interaction. Cells 2023; 12:306. [PMID: 36672241 PMCID: PMC9856966 DOI: 10.3390/cells12020306] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are versatile, post-transcriptional regulators of gene expression. Canonical miRNAs are generated through the two-step DROSHA- and DICER-mediated processing of primary miRNA (pri-miRNA) transcripts with optimal or suboptimal features for DROSHA and DICER cleavage and loading into Argonaute (AGO) proteins, whereas multiple hairpin-structured RNAs are encoded in the genome and could be a source of non-canonical miRNAs. Recent advances in miRNA biogenesis research have revealed details of the structural basis of miRNA processing and cluster assistance mechanisms that facilitate the processing of suboptimal hairpins encoded together with optimal hairpins in polycistronic pri-miRNAs. In addition, a deeper investigation of miRNA-target interaction has provided insights into the complexity of target recognition with distinct outcomes, including target-mediated miRNA degradation (TDMD) and cooperation in target regulation by multiple miRNAs. Therefore, the coordinated or network regulation of both miRNA biogenesis and miRNA-target interaction is prevalent in miRNA biology. Alongside recent advances in the mechanistic investigation of miRNA functions, this review summarizes recent findings regarding the ordered regulation of miRNA biogenesis and miRNA-target interaction.
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Affiliation(s)
- Shintaro Komatsu
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hiroki Kitai
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Nagoya 464-8601, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu 501-1193, Japan
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19
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Torrez RM, Ohi MD, Garner AL. Structural Insights into the Advances and Mechanistic Understanding of Human Dicer. Biochemistry 2023; 62:1-16. [PMID: 36534787 DOI: 10.1021/acs.biochem.2c00570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The RNase III endoribonuclease Dicer was discovered to be associated with cleavage of double-stranded RNA in 2001. Since then, many advances in our understanding of Dicer function have revealed that the enzyme plays a major role not only in microRNA biology but also in multiple RNA interference-related pathways. Yet, there is still much to be learned regarding Dicer structure-function in relation to how Dicer and Dicer-like enzymes initiate their cleavage reaction and release the desired RNA product. This Perspective describes the latest advances in Dicer structural studies, expands on what we have learned from this data, and outlines key gaps in knowledge that remain to be addressed. More specifically, we focus on human Dicer and highlight the intermediate processing steps where there is a lack of structural data to understand how the enzyme traverses from pre-cleavage to cleavage-competent states. Understanding these details is necessary to model Dicer's function as well as develop more specific microRNA-targeted therapeutics for the treatment of human diseases.
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Affiliation(s)
- Rachel M Torrez
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States.,Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States.,Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
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20
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Emerging Role of MicroRNA-30c in Neurological Disorders. Int J Mol Sci 2022; 24:ijms24010037. [PMID: 36613480 PMCID: PMC9819962 DOI: 10.3390/ijms24010037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are a class of small non-coding RNAs that negatively regulate the expression of target genes by interacting with 3' untranslated regions of target mRNAs to induce mRNA degradation and translational repression. The miR-30 family members are involved in the development of many tissues and organs and participate in the pathogenesis of human diseases. As a key member of the miR-30 family, miR-30c has been implicated in neurological disorders such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, and stroke. Mechanistically, miR-30c may act as a multi-functional regulator of different pathogenic processes such as autophagy, apoptosis, endoplasmic reticulum stress, inflammation, oxidative stress, thrombosis, and neurovascular function, thereby contributing to different disease states. Here, we review and discuss the biogenesis, gene regulation, and the role and mechanisms of action of miR-30c in several neurological disorders and therapeutic potential in clinics.
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21
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Structural and functional basis of mammalian microRNA biogenesis by Dicer. Mol Cell 2022; 82:4064-4079.e13. [DOI: 10.1016/j.molcel.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/21/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
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