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Hong Y, Wei R, Li C, Cai H, Chen E, Pan X, Zhang W. Establishment of virus-induced gene-silencing system in Juglans sigillata Dode and functional analysis of JsFLS2 and JsFLS4. Gene 2024; 913:148385. [PMID: 38493973 DOI: 10.1016/j.gene.2024.148385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Juglans sigillata Dode is one of the important tree species in southwest China, and it has significant economic and ecological value. However, there is still a lack of effective methods to identify the functional genes of J. sigillata. By verifying the model plant tobacco, the pTRV2::JsPDS vector was able to cause photobleaching. This study showed that photobleaching occurred 24 and 30 d after the silencing vector was infected with aseptic seedlings and fruits of J. sigillata, respectively. When the OD600 was 0.6, and the injection dose was 500 μL, the gene silencing efficiency of aseptic seedlings was the highest at 16.7 %, significantly better than other treatments. Moreover, when the OD600 was 0.8, and the injection dose was 500 μL, the gene silencing efficiency in the walnut fruit was the highest (20 %). In addition, the VIGS system was successfully used to silence JsFLS2 and JsFLS4 genes in J. sigillata. This study also showed that the flavonol content and gene expression in the treatment group were decreased compared to the control group. In addition, the proteins transcribed and translated from the JsFLS4 gene may have higher catalytic activity for dihydroquercetin. The above results indicate that the TRV-mediated VIGS system can be an ideal tool for studying J. sigillata gene function.
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Affiliation(s)
- Yanyang Hong
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Rong Wei
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Chunxiang Li
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Hu Cai
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Erjuan Chen
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China
| | - Xuejun Pan
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China; Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China.
| | - Wen'e Zhang
- College of Agriculture, Guizhou University, Jiaxiu South Road, Guiyang, Guizhou 550025, China.
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Ehsan A, Tanveer K, Azhar M, Zahra Naqvi R, Jamil M, Mansoor S, Amin I, Asif M. Evaluation of BG, NPR1, and PAL in cotton plants through Virus Induced gene silencing reveals their role in whitefly stress. Gene 2024; 908:148282. [PMID: 38360122 DOI: 10.1016/j.gene.2024.148282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Whitefly is one of the most hazardous insect pests that infests a wide range of host plants and causes huge damage to crop worldwide. In order to engineer plants resilient to whitefly stress, it is important to identify and validate the responsive genes by exploring the molecular dynamics of plants under stress conditions. In this study three genes BG, NPR1, and PAL genes have been studied in cotton for elucidating their role in whitefly stress response. Initially, insilico approach was utilized to investigate the domains and phylogeny of BG, NPR1 and PAL genes and found out that these genes showed remarkable resemblance in four cotton species Gossypium hirsutum, G. barbadense, G. arboreum, and G. raimondii. In BG proteins the main functional domain was X8 belonging to glycohydro superfamily, in NPR1 two main functional domains were BTB_POZ at N terminal and NPR1_like_C at C terminal. In PAL functional domain PLN was found which belongs to Lyase class I superfamily. The promoter analysis of these genes displayed enrichment of hormone, stress and stimuli responsive cis elements. Through Virus Induced Gene Silencing (VIGS), these genes were targeted and kept under whitefly infestation. Overall, the whitefly egg and nymph production were observed 60-70% less on gene down regulated plants as compared to control plants. The qPCR-based expression analysis of certain stress-responsive genes showed that in BG down regulated plants the elevated expression of these whitefly responsive genes was detected, in NPR1 down regulated plants JAZ1 and HSP were found up regulated, ERF1 and WRKY40 didn't show significant differential expression, while MAPK6 was slightly down regulated. In PAL down regulated plants ERF1 and JAZ1 showed elevated expression while others didn't show significant alternation. Differential expression in gene down-regulated plants showed that whitefly responsive genes act in a complex inter signaling pathway and their expression impact each other. This study provides valuable insight into the structural and functional analysis of important whitefly responsive genes BG, NPR1, and PAL. The results will pave a path to future development of whitefly resilient crops.
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Affiliation(s)
- Aiman Ehsan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Khurram Tanveer
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Maryam Azhar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Mahnoor Jamil
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad 38000, Pakistan.
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Nematian M, Noormohammadi Z, Rahimi P, Irani S, Arefian E. Exploring the potential of structural modeling and molecular docking for efficient siRNA screening: A promising approach to Combat viral mutants, with a focus on HIV-1. Biochem Biophys Res Commun 2024; 708:149769. [PMID: 38518723 DOI: 10.1016/j.bbrc.2024.149769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
RNA interference (RNAi) holds immense potential for sequence-specific downregulation of disease-related genes. Small interfering RNA (siRNA) therapy has made remarkable strides, with FDA approval for treating specific human diseases, showcasing its promising future in disease treatment. Designing highly efficient siRNAs is a critical step in this process. Previous studies have introduced various algorithms and parameters for siRNA design and scoring. However, these attempts have often fallen short of meeting all essential criteria or required modifications, resulting in variable and unclear effectiveness of screened siRNAs, particularly against viral mutants with non-conserved short sequences. In this study, we present a fully optimized siRNA screening system considering all necessary parameters. Notably, we highlight the critical role of molecular docking simulations between siRNA and two functional domains of the Argonaute protein (PAZ and PIWI) in identifying the most efficient siRNAs, since the appropriate interaction between the guide siRNA strand and the RISC complex is crucial. Through our stringent method, we designed approximately 50 potential siRNAs targeting the HIV-1 vpr gene. Evaluation through XTT, qRT-PCR, and flow cytometry analysis on RAW 264.7 macrophage stable cells revealed negligible cytotoxicity and exceptional gene-silencing efficiency at both the transcriptional and translational levels for the top-ranked screened siRNAs. Given the growing interest in siRNA-based therapeutics, we anticipate that the insights from this study will contribute to improving treatment strategies against mutant viruses, particularly HIV-1.
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Affiliation(s)
- Mohammad Nematian
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Noormohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Pooneh Rahimi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center (VVRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Wu N, Lan H, Huang M, Wang W, Liu J. [ GmAGB1 plays a positive regulatory role in soybean defense responses]. Sheng Wu Gong Cheng Xue Bao 2024; 40:1050-1064. [PMID: 38658148 DOI: 10.13345/j.cjb.230429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Heterotrimeric GTP-binding protein (G-proteins) complex, which consists of Gα, Gβ and Gγ subunits, plays critical roles in defense signaling. Arabidopsis genome contains only a single Gβ-encoding gene, AGB1. Loss function of AGB1 in Arabidopsis results in enhanced susceptibility to a wide range of pathogens. However, the function of soybean AGB1 in immunity has not been previously interrogated. Bioinformatic analysis indicated that there are four GmAGB1 homologous genes in soybean genome, sharing homology of 86%-97%. To overcome the functional redundancy of these GmAGB1 homologs, virus-induced gene silencing (VIGS) mediated by the bean pod mottle virus (BPMV) was used to silence these four genes simultaneously. As expected, these four GmAGB1 homologous genes were indeed silenced by a single BPMV-VIGS vector carrying a conserved fragments among these four genes. A dwarfed phenotype was observed in GmAGB1s-silenced soybean plants, suggesting that GmAGB1s play a crucial role in growth and development. Disease resistance analysis indicated that silencing GmAGB1s significantly compromised the resistance of soybean plants against Xanthomonas campestris pv. glycinea (Xag). This reduced resistance was correlated with the decreased accumulation of pathogen-induced reactive oxygen species (ROS) and the reduced activation of GmMPK3 in response to flg22, a conserved N-terminal peptide of flagellin protein. These results indicate that GmAGB1 functions as a positive regulator in disease resistance and GmAGB1 is indispensable for the ROS production and GmMPK3 activation induced by pathogen infection. Yeast two hybrid assay showed that GmAGB1 interacted with GmAGG1, suggesting that an evolutionary conserved heterotrimeric G protein complex similarly functions in soybean.
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Affiliation(s)
- Nan Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Hujiao Lan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Minjun Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Wenxu Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Jianzhong Liu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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Hashimi SM, Huang M, Chen Y, Liu J. [Silencing GmATG5 genes accelerated senescence and enhanced disease resistance in soybean]. Sheng Wu Gong Cheng Xue Bao 2024; 40:1065-1075. [PMID: 38658149 DOI: 10.13345/j.cjb.230452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Autophagy plays an essential role in recycling/re-utilizing nutrients and in adaptions to numerous stresses. However, the roles of autophagy in soybean have not been investigated extensively. In this study, a virus-induced gene silencing approach mediated by bean pod mottle virus (BPMV) was used to silence autophagy-related gene 5 (ATG5) genes in soybean (referred to as GmATG5). Our results showed that ATG8 proteins were massively accumulated in the dark-treated leaves of the GmATG5-silenced plants relative to the vector control plants (BPMV-0), indicating that autophagy pathway is impaired in the GmATG5-silenced plants. Consistent with the impaired autophagy, an accelerated senescence phenotype was observed on the leaves of the dark-treated GmATG5-silenced plants, which was not shown on the leaves of the dark-treated BPMV-0 plants. In addition, the accumulation levels of both reactive oxygen species (ROS) and salicylic acid (SA) were significantly induced in the GmATG5-silenced plants compared with that of the vector control plants (BPMV-0), indicating an activated immunity. Accordingly, the GmATG5-silenced plants exhibited significantly enhanced resistance against Pseudomonas syringae pv. glycinea (Psg) in comparison with the BPMV-0 plants. Nevertheless, the activated immunity observed in the GmATG5-silenced plant was independent of the activation of mitogen-activated protein kinase (MAPK).
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Affiliation(s)
- Said M Hashimi
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Minjun Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yu Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Jianzhong Liu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
- Institute of Genetics and Developmental Biology, College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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Hayashi J, Ochi Y, Senpuku K, Wada SI, Wada F, Harada-Shiba M, Urata H. Rational design of prodrug-type apoB-targeted siRNA for nuclease resistance improvement without compromising gene silencing potency. Bioorg Med Chem 2024; 104:117693. [PMID: 38552598 DOI: 10.1016/j.bmc.2024.117693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Synthetic siRNA molecules without chemical modifications are easily degraded in the body, and 2'-O-modifications are frequently introduced to enhance stability. However, such chemical modifications tend to impact the gene knockdown potency of siRNA negatively. To circumvent this problem, we previously developed a prodrug-type siRNA bearing 2'-O-methyldithiomethyl (MDTM) groups, which can be converted into unmodified siRNA under the reductive environment in cells. In this study, we developed a nuclease-resistant prodrug-type 2'-O-MDTM siRNA for deployment in future animal experiments. To rationally design siRNA modified with a minimal number of 2'-O-MDTM nucleotide residues, we identified the sites susceptible to nuclease digestion and tolerant to 2'-O-methyl (2'-OMe) modification in the antisense strand of apolipoprotein B-targeted siRNA. Subsequently, we optimized the positions where the 2'-OMe and 2'-O-MDTM groups should be incorporated. siRNA bearing the 2'-O-MDTM and 2'-OMe groups at their respective optimized positions exhibited efficient knockdown potency in vitro and enhanced stability in serum.
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Affiliation(s)
- Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Yosuke Ochi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Kota Senpuku
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Fumito Wada
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Mariko Harada-Shiba
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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De A, Kang JH, Sauraj, Lee OH, Ko YT. Optimizing long-term stability of siRNA using thermoassemble ionizable reverse pluronic-Bcl2 micelleplexes. Int J Biol Macromol 2024; 264:130783. [PMID: 38471603 DOI: 10.1016/j.ijbiomac.2024.130783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/26/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Thermosassemble Ionizable Reverse Pluronic (TIRP) platform stands out for its distinctive combination of thermoassemble and ionizable features, effectively overcoming challenges in previous siRNA delivery systems. This study opens up a formation for long-term stabilization, and high loading of siRNA, specifically crafted for targeting oncogenic pathways. TIRP-Bcl2 self-assembles into a unique micelle structure with a nanodiameter of 75.8 ± 5.7 nm, efficiently encapsulating Bcl2 siRNA while maintaining exceptional colloidal stability at 4 °C for 8 months, along with controlled release profiles lasting 180 h. The dual ionizable headgroup enhance the siRNA loading and the revers pluronic unique structural orientation enhance the stability of the siRNA. The thermoassemble of TIRP-Bcl2 facilitates flexi-rigid response to mild hyperthermia, enhancing deep tissue penetration and siRNA release in the tumor microenvironment. This responsive behavior improves intracellular uptake and gene silencing efficacy in cancer cells. TIRP, with its smaller particle size and reverse pluronic nature, efficiently transports siRNA across the blood-brain barrier, holding promise for revolutionizing glioblastoma (GBM) treatment. TIRP-Bcl2 shows significant potential for precise, personalized therapies, promising prolonged siRNA delivery and in vitro/in vivo stability. This research opens avenues for further exploration and clinical translation of this innovative nanocarrier system across different cancers.
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Affiliation(s)
- Anindita De
- College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, South Korea..
| | - Ji Hee Kang
- College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, South Korea
| | - Sauraj
- College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, South Korea
| | - O Hyun Lee
- College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, South Korea
| | - Young Tag Ko
- College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, South Korea..
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Xiong J, Liu Y, Wu P, Bian Z, Li B, Zhang Y, Zhu B. Identification and virus-induced gene silencing (VIGS) analysis of methyltransferase affecting tomato (Solanum lycopersicum) fruit ripening. Planta 2024; 259:109. [PMID: 38558186 DOI: 10.1007/s00425-024-04384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/09/2024] [Indexed: 04/04/2024]
Abstract
MAIN CONCLUSION Six methyltransferase genes affecting tomato fruit ripening were identified through genome-wide screening, VIGS assay, and expression pattern analysis. The data provide the basis for understanding new mechanisms of methyltransferases. Fruit ripening is a critical stage for the formation of edible quality and seed maturation, which is finely modulated by kinds of factors, including genetic regulators, hormones, external signals, etc. Methyltransferases (MTases), important genetic regulators, play vital roles in plant development through epigenetic regulation, post-translational modification, or other mechanisms. However, the regulatory functions of numerous MTases except DNA methylation in fruit ripening remain limited so far. Here, six MTases, which act on different types of substrates, were identified to affect tomato fruit ripening. First, 35 MTase genes with relatively high expression at breaker (Br) stage of tomato fruit were screened from the tomato MTase gene database encompassing 421 genes totally. Thereafter, six MTase genes were identified as potential regulators of fruit ripening via virus-induced gene silencing (VIGS), including four genes with a positive regulatory role and two genes with a negative regulatory role, respectively. The expression of these six MTase genes exhibited diverse patterns during the fruit ripening process, and responded to various external ripening-related factors, including ethylene, 1-methylcyclopropene (1-MCP), temperature, and light exposure. These results help to further elaborate the biological mechanisms of MTase genes in tomato fruit ripening and enrich the understanding of the regulatory mechanisms of fruit ripening involving MTases, despite of DNA MTases.
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Affiliation(s)
- Jiaxin Xiong
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Ye Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Peiwen Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Zheng Bian
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Bowen Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Yifan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
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Ghimire P, Motamedi M, Joh R. Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly. PLoS Comput Biol 2024; 20:e1012027. [PMID: 38598558 PMCID: PMC11034663 DOI: 10.1371/journal.pcbi.1012027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 04/22/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Although the length and constituting sequences for pericentromeric repeats are highly variable across eukaryotes, the presence of multiple pericentromeric repeats is one of the conserved features of the eukaryotic chromosomes. Pericentromeric heterochromatin is often misregulated in human diseases, with the expansion of pericentromeric repeats in human solid cancers. In this article, we have developed a mathematical model of the RNAi-dependent methylation of H3K9 in the pericentromeric region of fission yeast. Our model, which takes copy number as an explicit parameter, predicts that the pericentromere is silenced only if there are many copies of repeats. It becomes bistable or desilenced if the copy number of repeats is reduced. This suggests that the copy number of pericentromeric repeats alone can determine the fate of heterochromatin silencing in fission yeast. Through sensitivity analysis, we identified parameters that favor bistability and desilencing. Stochastic simulation shows that faster cell division and noise favor the desilenced state. These results show the unexpected role of pericentromeric repeat copy number in gene silencing and provide a quantitative basis for how the copy number allows or protects repetitive and unique parts of the genome from heterochromatin silencing, respectively.
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Affiliation(s)
- Puranjan Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Mo Motamedi
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, Boston, Massachusetts, United States of America
| | - Richard Joh
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Massey Cancer Center, Virginia Commonwealth University, Richmond Virginia, United States of America
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Planté-Bordeneuve V, Perrain V. Vutrisiran: a new drug in the treatment landscape of hereditary transthyretin amyloid polyneuropathy. Expert Opin Drug Discov 2024; 19:393-402. [PMID: 38281068 DOI: 10.1080/17460441.2024.2306843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 01/29/2024]
Abstract
INTRODUCTION Hereditary transthyretin (ATTRv) amyloidosis is a progressive, fatal disorder caused by mutations in the transthyretin (TTR) gene leading to deposition of the misfolded protein in amyloid fibrils. The main phenotypes are peripheral neuropathy (PN) and cardiomyopathy (CM). AREAS COVERED Gene silencing therapy, by dramatically reducing liver production of TTR, has transformed ATTRv-PN patient care in the last decade. In this drug discovery case history, the authors discuss the treatment history of ATTRv-PN and focus on the latest siRNA therapy: vutrisiran. Vutrisiran is chemically enhanced and N-acetylgalactosamin-conjugated, allowing increased stability and specific liver delivery. HELIOS-A, a phase III, multicenter randomized study, tested vutrisiran in ATTRv-PN and showed significant improvement in neuropathy impairment, disability, quality of life (QoL), gait speed, and nutritional status. Tolerance was acceptable, no safety signals were raised. EXPERT OPINION Vutrisiran offers a new treatment option for patients with ATTRv-PN. Vutrisian's easier delivery and administration route, at a quarterly frequency, as well as the absence of premedication, are major improvements to reduce patients' disease burden and improve their QoL. Its place in the therapeutic strategy is to be determined, considering affordability.
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Affiliation(s)
- Violaine Planté-Bordeneuve
- Department of Neurology, Henri Mondor University Hospital, AP-HP, Créteil, France
- Mondor Biomedical Research Institute - IMRB, INSERM, U955 Team 10 "Biology of the Neuromuscular System", Créteil, France
| | - Valentine Perrain
- Department of Neurology, Henri Mondor University Hospital, AP-HP, Créteil, France
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Tian L, Li J, Xu Y, Qiu Y, Zhang Y, Li X. A MAP kinase cascade broadly regulates the lifestyle of Sclerotinia sclerotiorum and can be targeted by HIGS for disease control. Plant J 2024; 118:324-344. [PMID: 38149487 DOI: 10.1111/tpj.16606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/15/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
Abstract
Sclerotinia sclerotiorum causes white mold or stem rot in a wide range of economically important plants, bringing significant yield losses worldwide. Control of this pathogen is difficult as its resting structure sclerotia can survive in soil for years, and no Resistance genes have been identified in S. sclerotiorum hosts. Host-induced gene silencing (HIGS) has shown promising effects in controlling many fungal pathogens, including S. sclerotiorum. However, better molecular genetic understanding of signaling pathways involved in its development and pathogenicity is needed to provide effective HIGS gene targets. Here, by employing a forward genetic screen, we characterized an evolutionarily conserved mitogen-activated protein kinase (MAPK) cascade in S. sclerotiorum, consisting of SsSte50-SsSte11-SsSte7-Smk1, which controls mycelial growth, sclerotia development, compound appressoria formation, virulence, and hyphal fusion. Moreover, disruption of the putative downstream transcription factor SsSte12 led to normal sclerotia but deformed appressoria and attenuated host penetration, as well as impaired apothecia formation, suggestive of diverged regulation downstream of the MAPK cascade. Most importantly, targeting SsSte50 using host-expressed double-stranded RNA resulted in largely reduced virulence of S. sclerotiorum on both Nicotiana benthamiana leaves and transgenic Arabidopsis thaliana plants. Therefore, this MAPK signaling cascade is generally needed for its growth, development, and pathogenesis and can serve as ideal HIGS targets for mitigating economic damages caused by S. sclerotiorum infection.
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Affiliation(s)
- Lei Tian
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Josh Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Yan Xu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Yilan Qiu
- Department of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yuelin Zhang
- College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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12
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Shu Q, Liu GC, He JW, Hu P, Dong ZW, Zhao RP, Zhang HR, Li XY. RNAi efficiency is enhanced through knockdown of double-stranded RNA-degrading enzymes in butterfly Papilio xuthus. Arch Insect Biochem Physiol 2024; 115:e22113. [PMID: 38628056 DOI: 10.1002/arch.22113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/27/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
The efficiency of RNA interference (RNAi) has always limited the research on the phenotype innovation of Lepidoptera insects. Previous studies have found that double-stranded RNA-degrading enzyme (dsRNase) is an important factor in RNAi efficiency, but there have been no relevant reports in butterflies (Papilionoidea). Papilio xuthus is one of the important models in butterflies with an extensive experimental application value. To explore the effect of dsRNase in the RNAi efficiency on butterflies, six dsRNase genes (PxdsRNase 1-6) were identified in P. xuthus genome, and their dsRNA-degrading activities were subsequently detected by ex vivo assays. The result shows that the dsRNA-degrading ability of gut content (<1 h) was higher than hemolymph content (>12 h). We then investigated the expression patterns of these PxdsRNase genes during different tissues and developmental stages, and related RNAi experiments were carried out. Our results show that different PxdsRNase genes had different expression levels at different developmental stages and tissues. The expression of PxdsRNase2, PxdsRNase3, and PxdsRNase6 were upregulated significantly through dsGFP injection, and PxdsRNase genes can be silenced effectively by injecting their corresponding dsRNA. RNAi-of-RNAi studies with PxEbony, which acts as a reporter gene, observed that silencing PxdsRNase genes can increase RNAi efficiency significantly. These results confirm that silencing dsRNase genes can improve RNAi efficiency in P. xuthus significantly, providing a reference for the functional study of insects such as butterflies with low RNAi efficiency.
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Affiliation(s)
- Qian Shu
- Yunnan Agricultural University College of Plant Protection, Kunming, Yunnan, China
| | - Gui-Chun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jin-Wu He
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ping Hu
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhi-Wei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruo-Ping Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Rui Zhang
- Yunnan Agricultural University College of Plant Protection, Kunming, Yunnan, China
| | - Xue-Yan Li
- Key Laboratory of Genetic Evolution & Animal Models, Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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13
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Shen H, Gu J, Liu X, Song M. Small nucleolar RNA host gene 1 silence inhibits the lipopolysaccharide-induced microglial apoptosis and inflammation. Cell Mol Biol (Noisy-le-grand) 2024; 70:182-186. [PMID: 38650136 DOI: 10.14715/cmb/2024.70.3.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Indexed: 04/25/2024]
Abstract
Microglia activation is an early mediator of neuroinflammation and a major contributor to spinal damage and motor dysfunction. This study was designed to investigate the role of small nucleolar RNA host gene 1 (SNHG1) on the apoptosis and inflammatory response of microglial cell BV-2 and its underlying molecular mechanism. The C5 lamina contusion-induced mouse model of spinal cord injury (SCI) was constructed. Mouse microglia BV2 was stimulated by lipopolysaccharide (LPS) to establish the in vitro model of SCI. The quantitative reverse transcription polymerase chain reaction method was used to quantify RNA expression levels. Enzyme-linked immunosorbent assays were used to quantify concentrations of inflammatory cytokines. Protein levels were assessed by western blotting, and apoptosis was assessed by flow cytometry. Dual luciferase reporter gene assay and RNA pull-down assay were conducted to investigate the binding relationships between molecules. Upregulation of SNHG1 and downregulation of miR-195-5p were observed in the spinal cords of SCI mouse model. LPS treatment led to elevation of SNHG1 expression in BV2 cells, as well as accelerated apoptosis and inflammation. Evident mitigation of LPS-induced BV2 cell damage was observed after SNHG1 knockdown. MiR-195-5p was identified as a target of SNHG1. Inhibition of miR-195-5p restored the impact of SNHG1 knockdown on cell damage of LPS-treated BV2 cells. Furthermore, miR-195-5p can target activating transcription factor-6 (ATF6). In summary, SNHG1 knockdown ameliorates LPS-induced microglial apoptosis and inflammatory response via the miR-195-5p/ATF6 axis, providing a novel direction for SCI treatment.
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Affiliation(s)
- Hongtao Shen
- The Fourth Department of Orthopaedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, PR China.
| | - Jiaao Gu
- The Fourth Department of Orthopaedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, PR China.
| | - Xing Liu
- The Fourth Department of Orthopaedics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, PR China.
| | - Mowei Song
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, PR China.
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14
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Figueroa-Bossi N, Fernández-Fernández R, Kerboriou P, Bouloc P, Casadesús J, Sánchez-Romero MA, Bossi L. Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin. Nat Commun 2024; 15:2787. [PMID: 38555352 PMCID: PMC10981669 DOI: 10.1038/s41467-024-47114-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negatively-supercoiled plectoneme to "unroll" disrupting the H-NS bridges and releasing H-NS.
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Affiliation(s)
- Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Rocío Fernández-Fernández
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Patricia Kerboriou
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | | | - Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France.
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15
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Cao D. RNA-directed DNA methylation as a weapon in parental conflict. Plant Physiol 2024; 194:1931-1933. [PMID: 38095352 PMCID: PMC10980382 DOI: 10.1093/plphys/kiad664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 04/01/2024]
Affiliation(s)
- Dechang Cao
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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16
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Straube H. Triterpene tales: Two genes involved in Nicotiana attenuata herbivore defense. Plant Physiol 2024; 194:2191-2193. [PMID: 38189946 PMCID: PMC10980509 DOI: 10.1093/plphys/kiae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024]
Affiliation(s)
- Henryk Straube
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Department of Plant and Environmental Sciences, Faculty of Science, Section for Plant Biochemistry, University of Copenhagen, 1871 Frederiksberg C, Copenhagen, Denmark
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17
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Rossi I, Marodin G, Lupo MG, Adorni MP, Papotti B, Dall’Acqua S, Ferri N. Gene Silencing of Angiopoietin-like 3 (ANGPTL3) Induced De Novo Lipogenesis and Lipid Accumulation in Huh7 Cell Line. Int J Mol Sci 2024; 25:3708. [PMID: 38612519 PMCID: PMC11011473 DOI: 10.3390/ijms25073708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Angiopoietin-like 3 (ANGPTL3) is a hepatokine acting as a negative regulator of lipoprotein lipase (LPL). Vupanorsen, an ANGPTL3 directed antisense oligonucleotide, showed an unexpected increase in liver fat content in humans. Here, we investigated the molecular mechanism linking ANGPTL3 silencing to hepatocyte fat accumulation. Human hepatocarcinoma Huh7 cells were treated with small interfering RNA (siRNA) directed to ANGPTL3, human recombinant ANGPTL3 (recANGPTL3), or their combination. Using Western blot, Oil Red-O, biochemical assays, and ELISA, we analyzed the expression of genes and proteins involved in lipid metabolism. Oil Red-O staining demonstrated that lipid content increased after 48 h of ANGPTL3 silencing (5.89 ± 0.33 fold), incubation with recANGPTL3 (4.08 ± 0.35 fold), or their combination (8.56 ± 0.18 fold), compared to untreated cells. This effect was also confirmed in Huh7-LX2 spheroids. A total of 48 h of ANGPTL3 silencing induced the expression of genes involved in the de novo lipogenesis, such as fatty acid synthase, stearoyl-CoA desaturase, ATP citrate lyase, and Acetyl-Coenzyme A Carboxylase 1 together with the proprotein convertase subtilisin/kexin 9 (PCSK9). Time-course experiments revealed that 6 h post transfection with ANGPTL3-siRNA, the cholesterol esterification by Acyl-coenzyme A cholesterol acyltransferase (ACAT) was reduced, as well as total cholesterol content, while an opposite effect was observed at 48 h. Under the same experimental conditions, no differences in secreted apoB and PCSK9 were observed. Since PCSK9 was altered by the treatment, we tested a possible co-regulation between the two genes. The effect of ANGPTL3-siRNA on the expression of genes involved in the de novo lipogenesis was not counteracted by gene silencing of PCSK9. In conclusion, our in vitro study suggests that ANGPTL3 silencing determines lipid accumulation in Huh7 cells by inducing the de novo lipogenesis independently from PCSK9.
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Affiliation(s)
- Ilaria Rossi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (I.R.); (G.M.); (S.D.)
| | - Giorgia Marodin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (I.R.); (G.M.); (S.D.)
| | | | - Maria Pia Adorni
- Department of Medicine and Surgery, University of Parma, Via Volturno 39/F, 43125 Parma, Italy;
| | - Bianca Papotti
- Department of Food and Drug, University of Parma, Viale delle Scienze 27/A, 43124 Parma, Italy;
| | - Stefano Dall’Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (I.R.); (G.M.); (S.D.)
| | - Nicola Ferri
- Department of Medicine, University of Padova, 35128 Padova, Italy;
- Veneto Institute of Molecular Medicine (VIMM), Via Orus, 2, 35129 Padova, Italy
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18
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Atanasoff-Kardjalieff AK, Berger H, Steinert K, Janevska S, Ponts N, Humpf HU, Kalinina S, Studt-Reinhold L. Incorporation of the histone variant H2A.Z counteracts gene silencing mediated by H3K27 trimethylation in Fusarium fujikuroi. Epigenetics Chromatin 2024; 17:7. [PMID: 38509556 PMCID: PMC10953111 DOI: 10.1186/s13072-024-00532-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Fusarium fujikuroi is a pathogen of rice causing diverse disease symptoms such as 'bakanae' or stunting, most likely due to the production of various natural products (NPs) during infection. Fusaria have the genetic potential to synthesize a plethora of these compounds with often diverse bioactivity. The capability to synthesize NPs exceeds the number of those being produced by far, implying a gene regulatory network decisive to induce production. One such regulatory layer is the chromatin structure and chromatin-based modifications associated with it. One prominent example is the exchange of histones against histone variants such as the H2A variant H2A.Z. Though H2A.Z already is well studied in several model organisms, its regulatory functions are not well understood. Here, we used F. fujikuroi as a model to explore the role of the prominent histone variant FfH2A.Z in gene expression within euchromatin and facultative heterochromatin. RESULTS Through the combination of diverse '-omics' methods, we show the global distribution of FfH2A.Z and analyze putative crosstalks between the histone variant and two prominent histone marks, i.e., H3K4me3 and H3K27me3, important for active gene transcription and silencing, respectively. We demonstrate that, if FfH2A.Z is positioned at the + 1-nucleosome, it poises chromatin for gene transcription, also within facultative heterochromatin. Lastly, functional characterization of FfH2A.Z overexpression and depletion mutants revealed that FfH2A.Z is important for wild type-like fungal development and secondary metabolism. CONCLUSION In this study, we show that the histone variant FfH2A.Z is a mark of positive gene transcription and acts independently of the chromatin state most likely through the stabilization of the + 1-nucleosome. Furthermore, we demonstrate that FfH2A.Z depletion does not influence the establishment of both H3K27me3 and H3K4me3, thus indicating no crosstalk between FfH2A.Z and both histone marks. These results highlight the manifold functions of the histone variant FfH2A.Z in the phytopathogen F. fujikuroi, which are distinct regarding gene transcription and crosstalk with the two prominent histone marks H3K27me3 and H3K4me3, as proposed for other model organisms.
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Affiliation(s)
- Anna K Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria
| | - Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria
| | - Katharina Steinert
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Slavica Janevska
- (Epi-)Genetic Regulation of Fungal Virulence, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, 07745, Jena, Germany
| | - Nadia Ponts
- INRAE, UR1264 Mycology and Food Safety (MycSA), Villenave d'Ornon, 33882, France
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Svetlana Kalinina
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria.
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19
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Ooi YJ, Huang C, Lau K, Chew SY, Park JG, Chan-Park MB. Nontoxic, Biodegradable Hyperbranched Poly(β-amino ester)s for Efficient siRNA Delivery and Gene Silencing. ACS Appl Mater Interfaces 2024; 16:14093-14112. [PMID: 38449351 DOI: 10.1021/acsami.3c10620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
RNA interference (RNAi)-mediated gene silencing is a promising therapeutic approach to treat various diseases, but safe and efficient delivery remains a major challenge to its clinical application. Non-viral gene vectors, such as poly(β-amino esters) (pBAEs), have emerged as a potential candidate due to their biodegradability, low toxicity profile, ease of synthesis, and high gene transfection efficiency for both DNA and siRNA delivery. However, achieving significant gene silencing using pBAEs often requires a large amount of polymer carrier (with polymer/siRNA weight ratio >100) or high siRNA dose (>100 nM), which might potentially exacerbate toxicity concerns during delivery. To overcome these barriers, we designed and optimized a series of hyperbranched pBAEs capable of efficiently condensing siRNA and achieving excellent silencing efficiency at a lower polymer/siRNA weight ratio (w/w) and siRNA dose. Through modulation of monomer combinations and branching density, we identified the top-performing hyperbranched pBAEs, named as h(A2B3)-1, which possess good siRNA condensation ability, low cytotoxicity, and high cellular uptake efficiency. Compared with Lipofectamine 2000, h(A2B3)-1 achieved lower cytotoxicity and higher siRNA silencing efficiency in HeLa cells at a polymer/siRNA weight ratio of 30 and 30 nM siRNA dose. Notably, h(A2B3)-1 enhanced the gene uptake in primary neural cells and effectively silenced the target gene in hard-to-transfect primary cortical neurons and oligodendrocyte progenitor cells, with gene knockdown efficiencies of 34.8 and 53.4% respectively. By incorporating a bioreducible disulfide compartment into the polymer backbone, the cytocompatibility of the h(A2B3)-1 was greatly enhanced while maintaining their good transfection efficiency. Together, the low cytotoxicity and high siRNA transfection efficiency of hyperbranched h(A2B3)-1 in this study demonstrated their great potential as a non-viral gene vector for efficient siRNA delivery and RNAi-mediated gene silencing. This provides valuable insight into the future development of safe and efficient non-viral siRNA delivery systems as well as their translation into clinical applications.
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Affiliation(s)
- Ying Jie Ooi
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
| | - Chongquan Huang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- Neuroscience@NTU, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore 637459, Singapore
| | - Kieran Lau
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
| | - Sing Yian Chew
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jong Gu Park
- Welgene Inc, 693, Namcheon-ro, Namcheon-myeon, Gyeongsan-si, Gyeongsangbuk-do 38695, Republic of Korea
| | - Mary B Chan-Park
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
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20
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Apostolopoulos A, Kawamoto N, Chow SYA, Tsuiji H, Ikeuchi Y, Shichino Y, Iwasaki S. dCas13-mediated translational repression for accurate gene silencing in mammalian cells. Nat Commun 2024; 15:2205. [PMID: 38467613 PMCID: PMC10928199 DOI: 10.1038/s41467-024-46412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Current gene silencing tools based on RNA interference (RNAi) or, more recently, clustered regularly interspaced short palindromic repeats (CRISPR)‒Cas13 systems have critical drawbacks, such as off-target effects (RNAi) or collateral mRNA cleavage (CRISPR‒Cas13). Thus, a more specific method of gene knockdown is needed. Here, we develop CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13). Owing to its tight association with mRNA, dCas13 serves as a physical roadblock for scanning ribosomes during translation initiation and does not affect mRNA stability. Guide RNAs covering the start codon lead to the highest efficacy regardless of the translation initiation mechanism: cap-dependent, internal ribosome entry site (IRES)-dependent, or repeat-associated non-AUG (RAN) translation. Strikingly, genome-wide ribosome profiling reveals the ultrahigh gene silencing specificity of CRISPRδ. Moreover, the fusion of a translational repressor to dCas13 further improves the performance. Our method provides a framework for translational repression-based gene silencing in eukaryotes.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05278 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K07016 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005h0001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- Pioneering Projects MEXT | RIKEN
- Pioneering Projects MEXT | RIKEN
- Exploratory Research Center on Life and Living Systems (ExCELLS), 23EX601
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Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hitomi Tsuiji
- Education and Research Division of Pharmacy, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi, 464-8650, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
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21
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Qian R, Wu M, Yang Z, Wu Y, Guo W, Zhou Z, Wang X, Li D, Lu Y. Rectifying artificial nanochannels with multiple interconvertible permeability states. Nat Commun 2024; 15:2051. [PMID: 38448408 PMCID: PMC10918189 DOI: 10.1038/s41467-024-46312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Transmembrane channels play a vital role in regulating the permeation process, and have inspired recent development of biomimetic channels. Herein, we report a class of artificial biomimetic nanochannels based on DNAzyme-functionalized glass nanopipettes to realize delicate control of channel permeability, whereby the surface wettability and charge can be tuned by metal ions and DNAzyme-substrates, allowing reversible conversion between different permeability states. We demonstrate that the nanochannels can be reversibly switched between four different permeability states showing distinct permeability to various functional molecules. By embedding the artificial nanochannels into the plasma membrane of single living cells, we achieve selective transport of dye molecules across the cell membrane. Finally, we report on the advanced functions including gene silencing of miR-21 in single cancer cells and selective transport of Ca2+ into single PC-12 cells. In this work, we provide a versatile tool for the design of rectifying artificial nanochannels with on-demand functions.
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Affiliation(s)
- Ruocan Qian
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Mansha Wu
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Weijie Guo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Zerui Zhou
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Xiaoyuan Wang
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Dawei Li
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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22
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Park SH, Lee DH, Kim SA. Exosome Secretion and Cellular Signaling Change in a Fabry Disease Cell Model Induced by Gene-silencing. In Vivo 2024; 38:567-573. [PMID: 38418159 PMCID: PMC10905446 DOI: 10.21873/invivo.13475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 03/01/2024]
Abstract
BACKGROUND/AIM Fabry disease (FD) is caused by α-galactosidase A (AGA) deficiency, which ultimately leads to the intracellular accumulation of globotriaosylceramide (Gb3). Exosomes play a role in maintaining cellular homeostasis by clearing damaged or toxic materials, including proteins. In the process of excessive accumulation of intracellular Gb3 in Fabry disease, it may be suggested that exosomal secretion of Gb3 increases to preserve cell homeostasis. This study sought to determine how exosomal secretion and cell signaling change in an FD cell model produced by gene silencing. MATERIALS AND METHODS HEK293T cells were transfected with plasmids carrying shRNA against the GLA gene to produce the FD cell model. A recombinant AGA, agalsidase-beta, was used to evaluate the effect of enzyme replacement therapy (ERT) on exosomal secretion and cell signaling. RESULTS Exosome secretion was significantly increased in the Fabry disease cell model compared to the control vector cell model, and significantly decreased after agalsidase-beta treatment. The FD cell model showed higher reactive oxygen species (ROS) production and p53 protein expression compared to the control vector cell model. CONCLUSION Increased exosomal secretion in Fabry disease may be a cellular mechanism to avoid excessive and cytotoxic accumulation of Gb3 in lysosomes through intracellular signaling, including increased p53 expression.
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Affiliation(s)
- Sang Hyun Park
- Department of Internal Medicine, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Dae Han Lee
- Department of Pharmacology, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, School of Medicine, Eulji University, Daejeon, Republic of Korea
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23
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Cai Y, Liu Z, Wang H, Meng H, Cao Y. Mesoporous Silica Nanoparticles Mediate SiRNA Delivery for Long-Term Multi- Gene Silencing in Intact Plants. Adv Sci (Weinh) 2024; 11:e2301358. [PMID: 38145358 PMCID: PMC10916655 DOI: 10.1002/advs.202301358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 11/03/2023] [Indexed: 12/26/2023]
Abstract
RNA interference (RNAi) is a powerful tool for understanding and manipulating signaling pathways in plant science, potentially facilitating the accelerated development of novel plant traits and crop yield improvement. The common strategy for delivering siRNA into intact plants using agrobacterium or viruses is complicated and time-consuming, limiting the application of RNAi in plant research. Here, a novel delivery method based on mesoporous silica nanoparticles (MSNs) is reported, which allows for the efficient delivery of siRNA into mature plant leaves via topical application without the aid of mechanical forces, achieving transient gene knockdown with up to 98% silencing efficiency at the molecular level. In addition, this method is nontoxic to plant leaves, enabling the repeated delivery of siRNA for long-term silencing. White spots and yellowing phenotypes are observed after spraying the MSN-siRNA complex targeted at phytoene desaturase and magnesium chelatase genes. After high light treatment, photobleaching phenotypes are also observed by spraying MSNs-siRNA targeted at genes into the Photosystem II repair cycle. Furthermore, the study demonstrated that MSNs can simultaneously silence multiple genes. The results suggest that MSN-mediated siRNA delivery is an effective tool for long-term multi-gene silencing, with great potential for application in plant functional genomic analyses and crop improvement.
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Affiliation(s)
- Yao Cai
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Zhujiang Liu
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Hang Wang
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Huan Meng
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
| | - Yuhong Cao
- Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and TechnologyChinese Academy of SciencesBeijing100190China
- School of Nano Science and TechnologyUniversity of Chinese Academy of SciencesBeijing100049China
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24
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Casali C, Galgano L, Zannino L, Siciliani S, Cavallo M, Mazzini G, Biggiogera M. Impact of heat and cold shock on epigenetics and chromatin structure. Eur J Cell Biol 2024; 103:151373. [PMID: 38016352 DOI: 10.1016/j.ejcb.2023.151373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Cells are continuously exposed to various sources of insults, among which temperature variations are extremely common. Epigenetic mechanisms, critical players in gene expression regulation, undergo alterations due to these stressors, potentially leading to health issues. Despite the significance of DNA methylation and histone modifications in gene expression regulation, their changes following heat and cold shock in human cells remain poorly understood. In this study, we investigated the epigenetic profiles of human cells subjected to hyperthermia and hypothermia, revealing significant variations. Heat shock primarily led to DNA methylation increments and epigenetic modifications associated with gene expression silencing. In contrast, cold shock presented a complex scenario, with both methylation and demethylation levels increasing, indicating different epigenetic responses to the opposite thermal stresses. These temperature-induced alterations in the epigenome, particularly their impact on chromatin structural organization, represent an understudied area that could offer important insights into genome function and potential prospects for therapeutic targets.
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Affiliation(s)
- Claudio Casali
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
| | - Luca Galgano
- Laboratory of Biochemistry, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Lorena Zannino
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Stella Siciliani
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Margherita Cavallo
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | | | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
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25
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Xiao Z, Liu Z, Zhang H, Yang A, Cheng L, Liu D, Jiang C, Yu S, Yang Z, Ren M, Geng R. Transcriptomics and virus-induced gene silencing identify defence-related genes during Ralstonia solanacearum infection in resistant and susceptible tobacco. Genomics 2024; 116:110784. [PMID: 38199265 DOI: 10.1016/j.ygeno.2024.110784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/03/2024] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
Bacterial wilt (BW) caused by Ralstonia solanacearum is a globally prevalent bacterial soil-borne disease. In this study, transcriptome sequencing were subjected to roots after infection with the R. solanacearum in the resistant and susceptible tobacco variety. DEGs that responded to R. solanacearum infection in both resistant and susceptible tobacco contributed to pectinase and peroxidase development and were enriched in plant hormone signal transduction, signal transduction and MAPK signalling pathway KEGG terms. Core DEGs in the resistant tobacco response to R. solanacearum infection were enriched in cell wall, membrane, abscisic acid and ethylene terms. qRT-PCR indicated that Nitab4.5_0004899g0110, Nitab4.5_0004234g0080 and Nitab4.5_0001439g0050 contributed to the response to R. solanacearum infection in different resistant and susceptible tobacco. Silencing the p450 gene Nitab4.5_0001439g0050 reduced tobacco resistance to bacterial wilt. These results improve our understanding of the molecular mechanism of BW resistance in tobacco and solanaceous plants.
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Affiliation(s)
- Zhiliang Xiao
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhengwen Liu
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Huifen Zhang
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Aiguo Yang
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lirui Cheng
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Dan Liu
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Caihong Jiang
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Zhixiao Yang
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Min Ren
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
| | - Ruimei Geng
- The Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
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26
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Fang R. Microbe-induced gene silencing explores interspecies RNAi and opens up possibilities of crop protection. Sci China Life Sci 2024; 67:626-628. [PMID: 38155277 DOI: 10.1007/s11427-023-2477-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/01/2023] [Indexed: 12/30/2023]
Affiliation(s)
- Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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27
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Shang B, Li C, Zhang X. How intrinsically disordered proteins order plant gene silencing. Trends Genet 2024; 40:260-275. [PMID: 38296708 PMCID: PMC10932933 DOI: 10.1016/j.tig.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) possess low sequence complexity of amino acids and display non-globular tertiary structures. They can act as scaffolds, form regulatory hubs, or trigger biomolecular condensation to control diverse aspects of biology. Emerging evidence has recently implicated critical roles of IDPs and IDR-contained proteins in nuclear transcription and cytoplasmic post-transcriptional processes, among other molecular functions. We here summarize the concepts and organizing principles of IDPs. We then illustrate recent progress in understanding the roles of key IDPs in machineries that regulate transcriptional and post-transcriptional gene silencing (PTGS) in plants, aiming at highlighting new modes of action of IDPs in controlling biological processes.
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Affiliation(s)
- Baoshuan Shang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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28
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Cappelluti MA, Mollica Poeta V, Valsoni S, Quarato P, Merlin S, Merelli I, Lombardo A. Durable and efficient gene silencing in vivo by hit-and-run epigenome editing. Nature 2024; 627:416-423. [PMID: 38418872 PMCID: PMC10937395 DOI: 10.1038/s41586-024-07087-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
Permanent epigenetic silencing using programmable editors equipped with transcriptional repressors holds great promise for the treatment of human diseases1-3. However, to unlock its full therapeutic potential, an experimental confirmation of durable epigenetic silencing after the delivery of transient delivery of editors in vivo is needed. To this end, here we targeted Pcsk9, a gene expressed in hepatocytes that is involved in cholesterol homeostasis. In vitro screening of different editor designs indicated that zinc-finger proteins were the best-performing DNA-binding platform for efficient silencing of mouse Pcsk9. A single administration of lipid nanoparticles loaded with the editors' mRNAs almost halved the circulating levels of PCSK9 for nearly one year in mice. Notably, Pcsk9 silencing and accompanying epigenetic repressive marks also persisted after forced liver regeneration, further corroborating the heritability of the newly installed epigenetic state. Improvements in construct design resulted in the development of an all-in-one configuration that we term evolved engineered transcriptional repressor (EvoETR). This design, which is characterized by a high specificity profile, further reduced the circulating levels of PCSK9 in mice with an efficiency comparable with that obtained through conventional gene editing, but without causing DNA breaks. Our study lays the foundation for the development of in vivo therapeutics that are based on epigenetic silencing.
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Affiliation(s)
| | - Valeria Mollica Poeta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Valsoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Piergiuseppe Quarato
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simone Merlin
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - Angelo Lombardo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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29
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Zhou P, G. C. B, Stolte F, Wu C. Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum. Appl Environ Microbiol 2024; 90:e0166523. [PMID: 38185820 PMCID: PMC10880640 DOI: 10.1128/aem.01665-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Gene inactivation by creating in-frame deletion mutations in Fusobacterium nucleatum is time consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPR interference (CRISPRi) system. This system employs the nuclease-inactive Streptococcus pyogenes Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single-guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes, ftsX and radD, which are pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline, ftsX suppression caused filamentous cell formation akin to chromosomal ftsX deletion, while targeting radD significantly reduced RadD protein levels, abolishing RadD-mediated coaggregation. The system was then extended to probe essential genes bamA and ftsZ, which are vital for outer membrane biogenesis and cell division. Impressively, bamA suppression disrupted membrane integrity and bacterial separation, stalling growth, while ftsZ targeting yielded elongated cells in broth with compromised agar growth. Further studies on F. nucleatum clinical strain CTI-2 and Fusobacterium periodonticum revealed reduced indole synthesis when targeting tnaA. Moreover, silencing clpB in F. periodonticum decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains.IMPORTANCEHow can we effectively investigate the gene functions in Fusobacterium nucleatum, given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPR interference (CRISPRi) system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and single-guide RNA expression is driven by the robust, constitutive rpsJ promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered genetically intractable strains like CTI-2 and Fusobacterium periodonticum. With CRISPRi's potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
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Affiliation(s)
- Peng Zhou
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Bibek G. C.
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Flynn Stolte
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
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30
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Hoogenboezem EN, Patel SS, Lo JH, Cavnar AB, Babb LM, Francini N, Gbur EF, Patil P, Colazo JM, Michell DL, Sanchez VM, McCune JT, Ma J, DeJulius CR, Lee LH, Rosch JC, Allen RM, Stokes LD, Hill JL, Vickers KC, Cook RS, Duvall CL. Structural optimization of siRNA conjugates for albumin binding achieves effective MCL1-directed cancer therapy. Nat Commun 2024; 15:1581. [PMID: 38383524 PMCID: PMC10881965 DOI: 10.1038/s41467-024-45609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
The high potential of siRNAs to silence oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, divalent lipid-conjugated siRNAs are optimized for in situ binding to albumin to improve pharmacokinetics and tumor delivery. Systematic variation of the siRNA conjugate structure reveals that the location of the linker branching site dictates tendency toward albumin association versus self-assembly, while the lipid hydrophobicity and reversibility of albumin binding also contribute to siRNA intracellular delivery. The lead structure increases tumor siRNA accumulation 12-fold in orthotopic triple negative breast cancer (TNBC) tumors over the parent siRNA. This structure achieves approximately 80% silencing of the anti-apoptotic oncogene MCL1 and yields better survival outcomes in three TNBC models than an MCL-1 small molecule inhibitor. These studies provide new structure-function insights on siRNA-lipid conjugate structures that are intravenously injected, associate in situ with serum albumin, and improve pharmacokinetics and tumor treatment efficacy.
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Affiliation(s)
- Ella N Hoogenboezem
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Shrusti S Patel
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Justin H Lo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ashley B Cavnar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren M Babb
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Eva F Gbur
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Prarthana Patil
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Juan M Colazo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Danielle L Michell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Violeta M Sanchez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua T McCune
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jinqi Ma
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Carlisle R DeJulius
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Linus H Lee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jonah C Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ryan M Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry D Stokes
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jordan L Hill
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kasey C Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Rebecca S Cook
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Craig L Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
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31
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Di Nardo M, Astigiano S, Baldari S, Pallotta MM, Porta G, Pigozzi S, Antonini A, Emionite L, Frattini A, Valli R, Toietta G, Soddu S, Musio A. The synergism of SMC1A cohesin gene silencing and bevacizumab against colorectal cancer. J Exp Clin Cancer Res 2024; 43:49. [PMID: 38365745 PMCID: PMC10870497 DOI: 10.1186/s13046-024-02976-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND SMC1A is a subunit of the cohesin complex that participates in many DNA- and chromosome-related biological processes. Previous studies have established that SMC1A is involved in cancer development and in particular, is overexpressed in chromosomally unstable human colorectal cancer (CRC). This study aimed to investigate whether SMC1A could serve as a therapeutic target for CRC. METHODS At first, we studied the effects of either SMC1A overexpression or knockdown in vitro. Next, the outcome of SMC1A knocking down (alone or in combination with bevacizumab, a monoclonal antibody against vascular endothelial growth factor) was analyzed in vivo. RESULTS We found that SMC1A knockdown affects cell proliferation and reduces the ability to grow in anchorage-independent manner. Next, we demonstrated that the silencing of SMC1A and the combo treatment were effective in increasing overall survival in a xenograft mouse model. Functional analyses indicated that both treatments lead to atypical mitotic figures and gene expression dysregulation. Differentially expressed genes were implicated in several pathways including gene transcription regulation, cellular proliferation, and other transformation-associated processes. CONCLUSIONS These results indicate that SMC1A silencing, in combination with bevacizumab, can represent a promising therapeutic strategy for human CRC.
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Affiliation(s)
- Maddalena Di Nardo
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy
| | | | - Silvia Baldari
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Maria Michela Pallotta
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy
| | - Giovanni Porta
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
| | - Simona Pigozzi
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate, Università degli Studi di Genova, Genoa, Italy
| | - Annalisa Antonini
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | | | - Annalisa Frattini
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Roberto Valli
- Dipartimento di Medicina e Chirurgia, Sezione di Biologia Generale e Genetica Medica, Università degli Studi dell'Insubria, Varese, Italy
| | - Gabriele Toietta
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Silvia Soddu
- Dipartimento Ricerca e Tecnologie Avanzate, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Antonio Musio
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Via Moruzzi, Pisa, 1 56124, Italy.
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Button AC, Hall SD, Ashley EL, McHugh CA. Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA. RNA 2024; 30:240-255. [PMID: 38164599 PMCID: PMC10870365 DOI: 10.1261/rna.079713.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of a human XIST-SPEN complex in vitro and identified novel sequence and structure determinants that may contribute to X chromosome silencing initiation. Binding of SPEN to XIST RNA requires RRM 4 of the protein, in contrast to the requirement of RRM 3 and RRM 4 for specific binding to SRA RNA. Measurements of SPEN binding to full-length, dimeric, trimeric, or other truncated versions of the A-repeat region revealed that high-affinity binding of XIST to SPEN in vitro requires a minimum of four A-repeat segments. SPEN binding to XIST A-repeat RNA changes the accessibility of the RNA at specific nucleotide sequences, as indicated by changes in RNA reactivity through chemical structure probing. Based on computational modeling, we found that inter-repeat duplexes formed by multiple A-repeats can present an unpaired adenosine in the context of a double-stranded region of RNA. The presence of this specific combination of sequence and structural motifs correlates with high-affinity SPEN binding in vitro. These data provide new information on the molecular basis of the XIST and SPEN interaction.
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Affiliation(s)
- Aileen C Button
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Simone D Hall
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Ethan L Ashley
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Colleen A McHugh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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Asohan J, Fakih HH, Das T, Sleiman HF. Control of the Assembly and Disassembly of Spherical Nucleic Acids Is Critical for Enhanced Gene Silencing. ACS Nano 2024; 18:3996-4007. [PMID: 38265027 DOI: 10.1021/acsnano.3c05940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Spherical nucleic acids─nanospheres with nucleic acids on their corona─have emerged as a promising class of nanocarriers, aiming to address the shortcomings of traditional nucleic therapeutics, namely, their poor stability, biodistribution, and cellular entry. By conjugating hydrophobic monomers to a growing nucleic acid strand in a sequence-defined manner, our group has developed self-assembled spherical nucleic acids (SaSNAs), for unaided, enhanced gene silencing. By virtue of their self-assembled nature, SaSNAs can disassemble under certain conditions in contrast to covalent or gold nanoparticle SNAs. Gene silencing involves multiple steps including cellular uptake, endosomal escape, and therapeutic cargo release. Whether assembly vs disassembly is advantageous to any of these steps has not been previously studied. In this work, we modify the DNA and hydrophobic portions of SaSNAs and examine their effects on stability, cellular uptake, and gene silencing. When the linkages between the hydrophobic units are changed from phosphate to phosphorothioate, we find that the SaSNAs disassemble better in endosomal conditions and exhibit more efficacious silencing, despite having cellular uptake similar to that of their phosphate counterparts. Thus, disassembly in the endolysosomal compartments is advantageous, facilitating the release of the nucleic acid cargo and the interactions between the hydrophobic units and endosomal lipids. We also find that SaSNAs partially disassemble in serum to bind albumin; the disassembled, albumin-bound strands are less efficient at cellular uptake and gene silencing than their assembled counterparts, which can engage scavenger receptors for internalization. When the DNA portion is cross-linked by G-quadruplex formation, disassembly decreases and cellular uptake significantly increases. However, this does not translate to greater gene silencing, again illustrating the need for disassembly of the SaSNAs when they are in the endosome. This work showcases the advantages of the dual nature of SaSNAs for gene silencing, requiring extracellular assembly and disassembly inside the cell compartments.
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Affiliation(s)
- Jathavan Asohan
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
| | - Hassan H Fakih
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
| | - Trishalina Das
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
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Perooli FM, Wilkinson KA, Pring K, Hanley JG. An essential role for the RNA helicase DDX6 in NMDA receptor-dependent gene silencing and dendritic spine shrinkage. Sci Rep 2024; 14:3066. [PMID: 38321143 PMCID: PMC10847504 DOI: 10.1038/s41598-024-53484-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024] Open
Abstract
MicroRNAs (miRNAs) repress translation of target mRNAs by associating with Argonaute (Ago) proteins in the RNA-induced silencing complex (RISC) to modulate protein expression. Specific miRNAs are required for NMDA receptor (NMDAR)-dependent synaptic plasticity by repressing the translation of proteins involved in dendritic spine morphogenesis. Rapid NMDAR-dependent silencing of Limk1 is essential for spine shrinkage and requires Ago2 phosphorylation at S387. Not all gene silencing events are modulated by S387 phosphorylation, and the mechanisms that govern the selection of specific mRNAs for silencing downstream of S387 phosphorylation are unknown. Here, we show that NMDAR-dependent S387 phosphorylation causes a rapid and transient increase in the association of Ago2 with Limk1, but not Apt1 mRNA. The specific increase in Limk1 mRNA binding to Ago2 requires recruitment of the helicase DDX6 to RISC. Furthermore, we show that DDX6 is required for NMDAR-dependent silencing of Limk1 via miR-134, but not Apt1 via miR-138, and is essential for NMDAR-dependent spine shrinkage. This work defines a novel mechanism for the rapid transduction of NMDAR stimulation into miRNA-mediated translational repression of specific genes to control dendritic spine morphology.
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Affiliation(s)
- Fathima M Perooli
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Kevin A Wilkinson
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Kate Pring
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Jonathan G Hanley
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.
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35
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Liu P, Wang K, Li J, Ogasawara MA, Xia Z, Wierda WG, Keating MJ, Li Y, Huang P. Global miRNA profiling reveals key molecules that contribute to different chronic lymphocytic leukemia incidences in Asian and Western populations. Haematologica 2024; 109:479-492. [PMID: 37646669 PMCID: PMC10828772 DOI: 10.3324/haematol.2023.283181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
It has been known for decades that the incidence of chronic lymphocytic leukemia (CLL) is significantly lower in Asia than in Western countries, but the reason responsible for this difference still remains a major knowledge gap. Using GeneChip® miRNA array to analyze the global microRNA expression in B lymphocytes from Asian and Western CLL patients and healthy individuals, we have identified microRNA with CLL-promoting or suppressive functions that are differentially expressed in Asian and Western individuals. In particular, miR-4485 is upregulated in CLL patients of both ethnic groups, and its expression is significantly lower in Asian healthy individuals. Genetic silencing of miR-4485 in CLL cells suppresses leukemia cell growth, whereas ectopic expression of miR-4485 promotes cell proliferation. Mechanistically, miR-4485 exerts its CLL-promoting activity by inhibiting the expression of TGR5 and activating the ERK1/2 pathway. In contrast, miR-138, miR-181a, miR- 181c, miR-181d, and miR-363 with tumor-suppressive function are highly expressed in Asian healthy individuals. Our study suggests that differential expression of several important microRNA with pro- or anti-CLL functions in Asian and Western B lymphocytes likely contributes to the difference in CLL incidence between the two ethnic groups, and that miR-4485 and its downstream molecule TGR5 could be potential therapeutic targets.
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Affiliation(s)
- Panpan Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou.
| | - Kefeng Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China; Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital,Sun Yat-sen University, Guangzhou
| | - Jianan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou
| | - Marcia A Ogasawara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Zhongjun Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou
| | - William G Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Michael J Keating
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Yiqing Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China; Department of Hematology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China.
| | - Peng Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou.
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Naresh M, Purkayastha A, Dasgupta I. P4 protein of an Indian isolate of rice tungro bacilliform virus modulates gene silencing. Virus Genes 2024; 60:55-64. [PMID: 38055154 DOI: 10.1007/s11262-023-02039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
Abstract
Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro bacilliform virus (RTBV), member of the family Caulimoviridae, genus Tungrovirus, species Tungrovirus oryzae, infects rice in South- and Southeast Asia and causes severe symptoms of stunting, yellow-orange discoloration and twisting of leaf tips. To better understand the possible counter-defensive roles of RTBV against the host RNAi defense system, we explored the ability of the P4 protein of an Indian isolate of RTBV to act as a possible modulator of RNAi. Using a transient silencing and silencing suppression assay in Nicotiana benthamiana, we show that P4 not only displays an RNAi suppressor function, but also potentially enhances RNAi. The results also suggests that the N-terminal 168 amino acid residues of P4 are sufficient to maintain RNAi suppressor activity. Taken together with the earlier reports this work strengthens the view that the P4 protein carries out RNAi suppressor and a potential RNAi enhancer function.
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Affiliation(s)
- Madhvi Naresh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Arunima Purkayastha
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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37
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Silvester E, Szoor B, Ivens A, Awuah-Mensah G, Gadelha C, Wickstead B, Matthews KR. A conserved trypanosomatid differentiation regulator controls substrate attachment and morphological development in Trypanosoma congolense. PLoS Pathog 2024; 20:e1011889. [PMID: 38408115 PMCID: PMC10919850 DOI: 10.1371/journal.ppat.1011889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/07/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Trypanosomatid parasites undergo developmental regulation to adapt to the different environments encountered during their life cycle. In Trypanosoma brucei, a genome wide selectional screen previously identified a regulator of the protein family ESAG9, which is highly expressed in stumpy forms, a morphologically distinct bloodstream stage adapted for tsetse transmission. This regulator, TbREG9.1, has an orthologue in Trypanosoma congolense, despite the absence of a stumpy morphotype in that parasite species, which is an important cause of livestock trypanosomosis. RNAi mediated gene silencing of TcREG9.1 in Trypanosoma congolense caused a loss of attachment of the parasites to a surface substrate in vitro, a key feature of the biology of these parasites that is distinct from T. brucei. This detachment was phenocopied by treatment of the parasites with a phosphodiesterase inhibitor, which also promotes detachment in the insect trypanosomatid Crithidia fasciculata. RNAseq analysis revealed that TcREG9.1 silencing caused the upregulation of mRNAs for several classes of surface molecules, including transferrin receptor-like molecules, immunoreactive proteins in experimental bovine infections, and molecules related to those associated with stumpy development in T. brucei. Depletion of TcREG9.1 in vivo also generated an enhanced level of parasites in the blood circulation consistent with reduced parasite attachment to the microvasculature. The morphological progression to insect forms of the parasite was also perturbed. We propose a model whereby TcREG9.1 acts as a regulator of attachment and development, with detached parasites being adapted for transmission.
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Affiliation(s)
- Eleanor Silvester
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Balazs Szoor
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Alasdair Ivens
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Georgina Awuah-Mensah
- Medical School, Centre for Genetics and Genomics, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Catarina Gadelha
- Medical School, Centre for Genetics and Genomics, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Bill Wickstead
- Medical School, Centre for Genetics and Genomics, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Keith R. Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
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Xu G, Law JA. Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation. Curr Opin Genet Dev 2024; 84:102147. [PMID: 38176333 PMCID: PMC10922829 DOI: 10.1016/j.gde.2023.102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome. This multilayered approach facilitates two essential, yet opposing functions, the ability to maintain heritable DNA methylation patterns while retaining the flexibility to modify these patterns during development.
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Affiliation(s)
- Guanghui Xu
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. https://twitter.com/@GuanghuiXu1
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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Tan YK, Castillo-Corea BRDJ, Kumar R, Lai PH, Lin SS, Wang HC. Shrimp SIRT4 promotes white spot syndrome virus replication. Fish Shellfish Immunol 2024; 145:109328. [PMID: 38142022 DOI: 10.1016/j.fsi.2023.109328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/01/2023] [Accepted: 12/20/2023] [Indexed: 12/25/2023]
Abstract
In WSSV pathogenesis, the molecular mechanisms and the key host factors that regulate the viral replication and morphogenesis remain unclear. However, like most viruses, WSSV is known to induce metabolic reprogramming in several metabolic pathways including the host glutamine metabolism, and several recent reports have suggested that the sirtuins SIRT3, SIRT4, and SIRT5, which belong to a family of NAD+-dependent deacetylases, play an important role in this regulation. Here we focus on characterizing LvSIRT4 from Litopenaeus vannamei and investigate its role in regulating glutamine dehydrogenase (GDH), an important enzyme that promotes glutaminolysis and viral replication. We found that LvSIRT4 silencing led to significant decreases in both WSSV gene expression and the number of viral genome copies. Conversely, overexpression of LvSIRT4 led to significant increases in the expression of WSSV genes and the WSSV genome copy number. Immunostaining in Sf9 insect cells confirmed the presence of LvSIRT4 in the mitochondria and the co-localization of LvSIRT4 and LvGDH in the same cellular locations. In vivo gene silencing of LvSIRT4 significantly reduced the gene expression of LvGDH whereas LvSIRT4 overexpression had no effect. However, neither silencing nor overexpression had any effect on the protein expression levels of LvGDH. Lastly, although GDH activity in uninfected shrimp was unchanged, the GDH enzyme activity in WSSV-infected shrimp was significantly increased after both LvSIRT4 silencing and overexpression. This suggests that although there may be no direct regulation, LvSIRT4 might still be able to indirectly regulate LvGDH via the mediation of one or more WSSV proteins that have yet to be identified.
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Affiliation(s)
- Yu Kent Tan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | | | - Ramya Kumar
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan; International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan.
| | - Ping-Hung Lai
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan; International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan.
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40
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Liu W, Cao J, Ma C, Zhou H, Guo T. Zinc(II)-Quinoline module and ROS cleavable crosslinker functionalized self-fluorescent siRNA vectors for selective gene silencing of cancer cells. J Control Release 2024; 366:366-374. [PMID: 38184231 DOI: 10.1016/j.jconrel.2023.12.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/27/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
A highly efficient siRNA vector (Zn-PQD) capable of selectively silencing genes in cancer cells was obtained by using ROS-cleavable DED to crosslink low molecular weight (LMW) polyethylene imine (PEI) modified by self-fluorescent metal coordinatied multifunctional module Zn-QS. Under the combined action of DED cross-linking and Zn-QS modification, Zn-PQD performs well in the siRNA delivery process in cancer cells, including siRNA condensation, cell uptake, endosome escape, and siRNA release. Zn-PQD exhibited higher transfection efficiency than commercial PEI25k and Lipo2k in multiple cancer cell lines including HepG2, HeLa, 4 T1, H520 and PANC-1, as well as cancer treatment-related stem cell rADSC. Ultimately, Zn-PQD can achieve extremely high and selective gene silencing effects in cancer cells (with a gene silencing rate of 98.3% in HepG2). This work is expected to provide an efficient and safe siRNA carrier for the future tumor siRNA therapy and its study of fluorescence mediated mechanism.
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Affiliation(s)
- Weijie Liu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Junpeng Cao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China
| | - Chunchao Ma
- Department of Neurology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China.
| | - Hao Zhou
- Department of Biochemistry and Molecular Biology, College of Life Science, Nankai University, Tianjin 300071, China
| | - Tianying Guo
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China.
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Sun L, Liu L, Song C, Wang Y, Jin QW. Heat stress-induced activation of MAPK pathway attenuates Atf1-dependent epigenetic inheritance of heterochromatin in fission yeast. eLife 2024; 13:e90525. [PMID: 38289024 PMCID: PMC10863984 DOI: 10.7554/elife.90525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024] Open
Abstract
Eukaryotic cells are constantly exposed to various environmental stimuli. It remains largely unexplored how environmental cues bring about epigenetic fluctuations and affect heterochromatin stability. In the fission yeast Schizosaccharomyces pombe, heterochromatic silencing is quite stable at pericentromeres but unstable at the mating-type (mat) locus under chronic heat stress, although both loci are within the major constitutive heterochromatin regions. Here, we found that the compromised gene silencing at the mat locus at elevated temperature is linked to the phosphorylation status of Atf1, a member of the ATF/CREB superfamily. Constitutive activation of mitogen-activated protein kinase (MAPK) signaling disrupts epigenetic maintenance of heterochromatin at the mat locus even under normal temperature. Mechanistically, phosphorylation of Atf1 impairs its interaction with heterochromatin protein Swi6HP1, resulting in lower site-specific Swi6HP1 enrichment. Expression of non-phosphorylatable Atf1, tethering Swi6HP1 to the mat3M-flanking site or absence of the anti-silencing factor Epe1 can largely or partially rescue heat stress-induced defective heterochromatic maintenance at the mat locus.
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Affiliation(s)
- Li Sun
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Libo Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Chunlin Song
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Yamei Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Quan-wen Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
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42
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Zhong C, Wang W, Liao L, Liu J. [Silencing GmWRKY33B genes leads to reduced disease resistance in soybean]. Sheng Wu Gong Cheng Xue Bao 2024; 40:163-176. [PMID: 38258639 DOI: 10.13345/j.cjb.230226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The WRKYs are a group of plant-specific transcription factors that play important roles in defense responses. In this study, we silenced 2 GmWRKY33B homologous genes using a bean pod mosaic virus (BPMV) vector carrying a single fragment from the conserved region of the GmWRKY33B genes. Silencing GmWRKY33B did not result in morphological changes. However, significantly reduced resistances to Pseudomonas syringae pv. glycinea (Psg) and soybean mosaic virus (SMV) were observed in the GmWRKY33B-silenced plants, indicating a positive role of the GmWRKY33B genes in disease resistance. Kinase assay showed that silencing the GmWRKY33B genes significantly reduced the activation of GmMPK6, but not GmMPK3, in response to flg22 treatment. Reverse transcriptase PCR (RT-PCR) analysis of the genes encoding prenyltransferases (PTs), which are the key enzymes in the biosynthesis of glyceollin, showed that the Psg-induced expression of these genes was significantly reduced in the GmWRKY33B-silenced plants compared with the BPMV-0 empty vector plants, which correlated with the presence of the W-boxes in the promoter regions of these genes. Taken together, our results suggest that GmWRKY33Bs are involved in soybean immunity through regulating the activation of the kinase activity of GmMPK6 as well as through regulating the expression of the key genes encoding the biosynthesis of glyceollins.
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Affiliation(s)
- Chenli Zhong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Wenxu Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Lina Liao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Jianzhong Liu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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43
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Nielsen M, Menon G, Zhao Y, Mateo-Bonmati E, Wolff P, Zhou S, Howard M, Dean C. COOLAIR and PRC2 function in parallel to silence FLC during vernalization. Proc Natl Acad Sci U S A 2024; 121:e2311474121. [PMID: 38236739 PMCID: PMC10823242 DOI: 10.1073/pnas.2311474121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Noncoding transcription induces chromatin changes that can mediate environmental responsiveness, but the causes and consequences of these mechanisms are still unclear. Here, we investigate how antisense transcription (termed COOLAIR) interfaces with Polycomb Repressive Complex 2 (PRC2) silencing during winter-induced epigenetic regulation of Arabidopsis FLOWERING LOCUS C (FLC). We use genetic and chromatin analyses on lines ineffective or hyperactive for the antisense pathway in combination with computational modeling to define the mechanisms underlying FLC repression. Our results show that FLC is silenced through pathways that function with different dynamics: a COOLAIR transcription-mediated pathway capable of fast response and in parallel a slow PRC2 switching mechanism that maintains each allele in an epigenetically silenced state. Components of both the COOLAIR and PRC2 pathways are regulated by a common transcriptional regulator (NTL8), which accumulates by reduced dilution due to slow growth at low temperature. The parallel activities of the regulatory steps, and their control by temperature-dependent growth dynamics, create a flexible system for registering widely fluctuating natural temperature conditions that change year on year, and yet ensure robust epigenetic silencing of FLC.
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Affiliation(s)
- Mathias Nielsen
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Govind Menon
- Computational and Systems Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Yusheng Zhao
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Eduardo Mateo-Bonmati
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Philip Wolff
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Shaoli Zhou
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
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44
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Ma YF, Liu TT, Zhao YQ, Luo J, Feng HY, Zhou YY, Gong LL, Zhang MQ, He YY, Hull JJ, Dewer Y, He M, He P. RNA Interference-Screening of Potentially Lethal Gene Targets in the White-Backed Planthopper Sogatella furcifera via a Spray-Induced and Nanocarrier-Delivered Gene Silencing System. J Agric Food Chem 2024; 72:1007-1016. [PMID: 38166405 DOI: 10.1021/acs.jafc.3c05659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
RNA interference (RNAi) is a widespread post-transcriptional silencing mechanism that targets homologous mRNA sequences for specific degradation. An RNAi-based pest management strategy is target-specific and considered a sustainable biopesticide. However, the specific genes targeted and the efficiency of the delivery methods can vary widely across species. In this study, a spray-induced and nanocarrier-delivered gene silencing (SI-NDGS) system that incorporated gene-specific dsRNAs targeting conserved genes was used to evaluate phenotypic effects in white-backed planthopper (WBPH). At 2 days postspraying, transcript levels for all target genes were significantly reduced and knockdown of two gene orthologs, hsc70-3 and PP-α, resulted in an elevated mortality (>60%) and impaired ecdysis. These results highlight the utility of the SI-NDGS system for identifying genes involved in WBPH growth and development that could be potentially exploitable as high mortality target genes to develop an alternative method for WBPH control.
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Affiliation(s)
- Yun-Feng Ma
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Ting-Ting Liu
- Qianxinan Agricultural Technology Extension Center, Xingyi 562404, P. R. China
| | - Ya-Qin Zhao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Juan Luo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Hong-Yan Feng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Yang-Yuntao Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Lang-Lang Gong
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Meng-Qi Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Yin-Yin He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - J Joe Hull
- USDA-ARS Arid Land Agricultural Research Center, Maricopa, Arizona 20250,United States
| | - Youssef Dewer
- Phytotoxicity Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, 7 Nadi El-Seid Street, Dokki 12618, Giza, Egypt
| | - Ming He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
| | - Peng He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, P. R. China
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45
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Yuan AH, Moazed D. Minimal requirements for the epigenetic inheritance of engineered silent chromatin domains. Proc Natl Acad Sci U S A 2024; 121:e2318455121. [PMID: 38198529 PMCID: PMC10801849 DOI: 10.1073/pnas.2318455121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
Mechanisms enabling genetically identical cells to differentially regulate gene expression are complex and central to organismal development and evolution. While gene silencing pathways involving DNA sequence-specific recruitment of histone-modifying enzymes are prevalent in nature, examples of sequence-independent heritable gene silencing are scarce. Studies of the fission yeast Schizosaccharomyces pombe indicate that sequence-independent propagation of heterochromatin can occur but requires numerous multisubunit protein complexes and their diverse activities. Such complexity has so far precluded a coherent articulation of the minimal requirements for heritable gene silencing by conventional in vitro reconstitution approaches. Here, we take an unconventional approach to defining these requirements by engineering sequence-independent silent chromatin inheritance in budding yeast Saccharomyces cerevisiae cells. The mechanism conferring memory upon these cells is remarkably simple and requires only two proteins, one that recognizes histone H3 lysine 9 methylation (H3K9me) and catalyzes the deacetylation of histone H4 lysine 16 (H4K16), and another that recognizes deacetylated H4K16 and catalyzes H3K9me. Together, these bilingual "read-write" proteins form an interdependent positive feedback loop that is sufficient for the transmission of DNA sequence-independent silent information over multiple generations.
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Affiliation(s)
- Andy H. Yuan
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Danesh Moazed
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
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46
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Ruf A, Robatzek S. "Messenger RNA just entered the chat": The next layer of cross-kingdom RNA transfer. Cell Host Microbe 2024; 32:7-8. [PMID: 38211564 DOI: 10.1016/j.chom.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024]
Abstract
Infectious fungi send small RNAs into plant cells to enhance their virulence by silencing defense-related genes. In this issue of Cell Host & Microbe, Wang and colleagues show that full-length messenger RNA is transported in vesicles from plants to fungi, becoming translated by fungal ribosomes and reducing fungal pathogenicity.
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Affiliation(s)
- Alessa Ruf
- LMU Munich Biocenter, Großhadener Strasse 4, 82152 Planegg, DE, Germany
| | - Silke Robatzek
- LMU Munich Biocenter, Großhadener Strasse 4, 82152 Planegg, DE, Germany.
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47
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Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell 2024; 187:110-129.e31. [PMID: 38181737 PMCID: PMC10783549 DOI: 10.1016/j.cell.2023.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/01/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
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Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tsotne Chitiashvili
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Y X Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yolanda Markaki
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Amanda J Collier
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guohao Liang
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jarrett Miller
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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48
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Torres JR, Botto JF, Sanchez DH. Canonical transcriptional gene silencing may contribute to long-term heat response and recovery through MOM1. Plant Cell Environ 2024; 47:372-382. [PMID: 37712454 DOI: 10.1111/pce.14722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/28/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Plant canonical transcriptional gene silencing (TGS) is involved in epigenetic mechanisms that mediate genomic imprinting and the suppression of transposable elements (TEs). It has been recognised that long-term heat disrupts epigenetic silencing, with the ensuing activation of TEs. However, the physiological involvement of the TGS machinery under prolonged high temperatures has not yet been established. Here, we performed non-lethal extended periodic heat stress and recovery treatments on Arabidopsis thaliana lines mutated on key TGS factors, analysing transcriptomic changes of coding-protein genes and TEs. Plants bearing MET1, DRM2 and CMT3, and MOM1 mutated alleles showed novel transcriptional properties compatible with functionalities concerning the induction/repression of partially shared or private heat-triggered transcriptome networks. Certain observations supported the idea that some responses are based on thermal de-silencing. TEs transcriptional activation uncovered the interaction with specific epigenetic layers, which may play dedicated suppressing roles under determinate physiological conditions such as heat. Furthermore, physiological experimentation suggested that MOM1 is required to resume growth after stress. Our data thus provide initial evidence that at least one canonical TGS factor may contribute to plant acclimation and recovery from non-lethal long-term heat despite the stress-induced epigenetic disturbance.
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Affiliation(s)
- José Roberto Torres
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier F Botto
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego H Sanchez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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49
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Müller I, Helin K. Keep quiet: the HUSH complex in transcriptional silencing and disease. Nat Struct Mol Biol 2024; 31:11-22. [PMID: 38216658 DOI: 10.1038/s41594-023-01173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/23/2023] [Indexed: 01/14/2024]
Abstract
The human silencing hub (HUSH) complex is an epigenetic repressor complex whose role has emerged as an important guardian of genome integrity. It protects the genome from exogenous DNA invasion and regulates endogenous retroelements by recruiting histone methyltransferases catalyzing histone 3 lysine 9 trimethylation (H3K9me3) and additional proteins involved in chromatin compaction. In particular, its regulation of transcriptionally active LINE1 retroelements, by binding to and neutralizing LINE1 transcripts, has been well characterized. HUSH is required for mouse embryogenesis and is associated with disease, in particular cancer. Here we provide insights into the structural and biochemical features of the HUSH complex. Furthermore, we discuss the molecular mechanisms by which the HUSH complex is recruited to specific genomic regions and how it silences transcription. Finally, we discuss the role of HUSH complex members in mammalian development, antiretroviral immunity, and diseases such as cancer.
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Affiliation(s)
- Iris Müller
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- The Institute of Cancer Research, London, UK.
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50
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Spatola Rossi T, Fricker M, Kriechbaumer V. Gene Stacking and Stoichiometric Expression of ER-Targeted Constructs Using "2A" Self-Cleaving Peptides. Methods Mol Biol 2024; 2772:337-351. [PMID: 38411827 DOI: 10.1007/978-1-0716-3710-4_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Simultaneous stoichiometric expression of multiple genes plays a major part in modern research and biotechnology. Traditional methods for incorporating multiple transgenes (or "gene stacking") have drawbacks such as long time frames, uneven gene expression, gene silencing, and segregation derived from the use of multiple promoters. 2A self-cleaving peptides have emerged over the last two decades as a functional gene stacking method and have been used in plants for the co-expression of multiple genes under a single promoter. Here we describe design features of multicistronic polyproteins using 2A peptides for co-expression in plant cells and targeting to the endoplasmic reticulum (ER). We designed up to quad-cistronic vectors that could target proteins in tandem to the ER. We also exemplify the incorporation of self-excising intein domains within 2A polypeptides, to remove residue additions. These features could aid in the design of stoichiometric protein co-expression strategies in plants in combination with targeting to different subcellular compartments.
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Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Mark Fricker
- Department of Biology, University of Oxford, Oxford, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
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