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Noguchi S, Ohkura S, Negishi Y, Tozawa S, Takizawa T, Morita R, Takahashi H, Ohkuchi A, Takizawa T. Cytoplasmic and nuclear DROSHA in human villous trophoblasts. J Reprod Immunol 2024; 162:104189. [PMID: 38241848 DOI: 10.1016/j.jri.2023.104189] [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: 11/01/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/21/2024]
Abstract
In villous trophoblasts, DROSHA is a key ribonuclease III enzyme that processes pri-microRNAs (pri-miRNAs) into pre-miRNAs at the placenta-specific, chromosome 19 miRNA cluster (C19MC) locus. However, little is known of its other functions. We performed formaldehyde crosslinking, immunoprecipitation, and sequencing (fCLIP-seq) analysis of terminal chorionic villi to identify DROSHA-binding RNAs in villous trophoblasts. In villous trophoblasts, DROSHA predominantly generated placenta-specific C19MC pre-miRNAs, including antiviral C19MC pre-miRNAs. The fCLIP-seq analysis also identified non-miRNA transcripts with hairpin structures potentially capable of binding to DROSHA (e.g., SNORD100 and VTRNA1-1). Moreover, in vivo immunohistochemical analysis revealed DROSHA in the cytoplasm of villous trophoblasts. DROSHA was abundant in the cytoplasm of villous trophoblasts, particularly in the apical region of syncytiotrophoblast, in the full-term placenta. Furthermore, in BeWo trophoblasts infected with Sindbis virus (SINV), DROSHA translocated to the cytoplasm and recognized the genomic RNA of SINV. Therefore, in trophoblasts, DROSHA not only regulates RNA metabolism, including the biogenesis of placenta-specific miRNAs, but also recognizes viral RNAs. After SINV infection, BeWo DROSHA-binding VTRNA1-1 was significantly upregulated, and cellular VTRNA1-1 was significantly downregulated, suggesting that DROSHA soaks up VTRNA1-1 in response to viral infection. These results suggest that the DROSHA-mediated recognition of RNAs defends against viral infection in villous trophoblasts. Our data provide insight into the antiviral functions of DROSHA in villous trophoblasts of the human placenta.
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Affiliation(s)
- Syunya Noguchi
- Department of Molecular Medicine and Anatomy, Nippon Medical School, Tokyo 113-8602, Japan
| | - Sadayuki Ohkura
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Yasuyuki Negishi
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Shohei Tozawa
- Department of Molecular Medicine and Anatomy, Nippon Medical School, Tokyo 113-8602, Japan; Department of Obstetrics and Gynecology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Takami Takizawa
- Department of Molecular Medicine and Anatomy, Nippon Medical School, Tokyo 113-8602, Japan
| | - Rimpei Morita
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Hironori Takahashi
- Department of Obstetrics and Gynecology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Akihide Ohkuchi
- Department of Obstetrics and Gynecology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Toshihiro Takizawa
- Department of Molecular Medicine and Anatomy, Nippon Medical School, Tokyo 113-8602, Japan.
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Hernandez Hernandez D, Ding L, Murao A, Dahlin LR, Li G, Arnolds KL, Amezola M, Klein A, Mitra A, Mecacci S, Linger JG, Guarnieri MT, Suzuki Y. Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs. ACS Synth Biol 2023; 12:2778-2782. [PMID: 37582217 PMCID: PMC10510714 DOI: 10.1021/acssynbio.3c00183] [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: 03/28/2023] [Indexed: 08/17/2023]
Abstract
Synergistic and supportive interactions among genes can be incorporated in engineering biology to enhance and stabilize the performance of biological systems, but combinatorial numerical explosion challenges the analysis of multigene interactions. The incorporation of DNA barcodes to mark genes coupled with next-generation sequencing offers a solution to this challenge. We describe improvements for a key method in this space, CombiGEM, to broaden its application to assembling typical gene-sized DNA fragments and to reduce the cost of sequencing for prevalent small-scale projects. The expanded reach of the method beyond currently targeted small RNA genes promotes the discovery and incorporation of gene synergy in natural and engineered processes such as biocontainment, the production of desired compounds, and previously uncharacterized fundamental biological mechanisms.
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Affiliation(s)
- Diana Hernandez Hernandez
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Lin Ding
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Ayako Murao
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Lukas R. Dahlin
- National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gabriella Li
- National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | | | - Melissa Amezola
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Amit Klein
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
- Department
of Bioengineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Aishwarya Mitra
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
- Department
of Bioengineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Sonia Mecacci
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Jeffrey G. Linger
- National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | | | - Yo Suzuki
- Synthetic
Biology and Bioenergy Group, J. Craig Venter
Institute, La Jolla, California 92037, United States
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Construction and verification of an infectious cDNA clone of coxsackievirus B5. Virol Sin 2022; 37:469-471. [PMID: 35288348 PMCID: PMC9707635 DOI: 10.1016/j.virs.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/07/2022] [Indexed: 12/14/2022] Open
Abstract
An infectious cDNA clone of CV-B5 was
constructed. The rescued and parental virus possessed similar
biological characteristics. The virulence of the rescued virus was similiar to
that of the parental virus. Viral distribution and tissue tropism of those two
viruses were in agreement.
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Lindenbach BD. Reinventing positive-strand RNA virus reverse genetics. Adv Virus Res 2022; 112:1-29. [PMID: 35840179 PMCID: PMC9273853 DOI: 10.1016/bs.aivir.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Reverse genetics is the prospective analysis of how genotype determines phenotype. In a typical experiment, a researcher alters a viral genome, then observes the phenotypic outcome. Among RNA viruses, this approach was first applied to positive-strand RNA viruses in the mid-1970s and over nearly 50 years has become a powerful and widely used approach for dissecting the mechanisms of viral replication and pathogenesis. During this time the global health importance of two virus groups, flaviviruses (genus Flavivirus, family Flaviviridae) and betacoronaviruses (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), have dramatically increased, yet these viruses have genomes that are technically challenging to manipulate. As a result, several new techniques have been developed to overcome these challenges. Here I briefly review key historical aspects of positive-strand RNA virus reverse genetics, describe some recent reverse genetic innovations, particularly as applied to flaviviruses and coronaviruses, and discuss their benefits and limitations within the larger context of rigorous genetic analysis.
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