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Li M, Li J, Zhang Y, Zhai Y, Chen Y, Lin L, Peng J, Zheng H, Chen J, Yan F, Lu Y. Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa. MOLECULAR PLANT PATHOLOGY 2024; 25:e13446. [PMID: 38502176 PMCID: PMC10950023 DOI: 10.1111/mpp.13446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about changes in chromatin accessibility of plants infected by viruses and its potential impact. Here, rice infected by rice stripe virus (RSV) was used to investigate virus-induced changes in chromatin accessibility. Our analysis identified a total of 6462 open- and 3587 closed-differentially accessible chromatin regions (DACRs) in rice under RSV infection by ATAC-seq. Additionally, by integrating ATAC-seq and RNA-seq, 349 up-regulated genes in open-DACRs and 126 down-regulated genes in closed-DACRs were identified, of which 34 transcription factors (TFs) were further identified by search of upstream motifs. Transcription levels of eight of these TFs were validated by reverse transcription-PCR. Importantly, four of these TFs (OsWRKY77, OsWRKY28, OsZFP12 and OsERF91) interacted with RSV proteins and are therefore predicted to play important roles in RSV infection. This is the first application of ATAC-seq and RNA-seq techniques to analyse changes in rice chromatin accessibility caused by RSV infection. Integrating ATAC-seq and RNA-seq provides a new approach to select candidate TFs in response to virus infection.
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Affiliation(s)
- Miaomiao Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jing Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yushan Zhai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Lin Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jianping Chen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
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2
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Wang G, Jiang G, Peng R, Wang Y, Li J, Sima Y, Xu S. Multi-omics integrative analysis revealed characteristic changes in blood cell immunity and amino acid metabolism in a silkworm model of hyperproteinemia. Int J Biol Macromol 2024; 258:128809. [PMID: 38128801 DOI: 10.1016/j.ijbiomac.2023.128809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Hyperproteinemia is a serious metabolic disease of both humans and animals characterized by an abnormally high plasma protein concentration (HPPC). Although hyperproteinemia can cause an imbalance in blood cell homeostasis, the functional changes to blood cells remain unclear. Here, a HPPC silkworm model was used to assess changes to the chromatin accessibility and transcript levels of genes related to blood cell metabolism and immune function. The results showed that HPPC enhanced phagocytosis of blood cells, increased chromatin accessibility and transcript levels of genes involved in cell phagocytosis, proliferation, stress, and programmed death, while genes associated with aromatic amino acid metabolism, and antibacterial peptide synthesis were inhibited in blood cells. Further analysis of the chromatin accessibility of the promoter region found that the high chromatin accessibility of genes sensitive to HPPC, was related to histone modifications, including tri-methylation of lysine residue 4 of histone H3 and acetylation of lysine residue 27 of histone H3. Changes to the chromatin accessibility and transcript levels of genes related to immune function and amino acid metabolism in the blood cells of the HPPC silkworm model provided useful references for future studies of the mechanisms underlying epigenomic regulation mediated by hyperproteinemia.
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Affiliation(s)
- Guang Wang
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou 215123, China
| | - Guihua Jiang
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou 215123, China
| | - Ruji Peng
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou 215123, China
| | - Yongfeng Wang
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou 215123, China
| | - Jianglan Li
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou 215123, China
| | - Yanghu Sima
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou 215123, China
| | - Shiqing Xu
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China; Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou 215123, China.
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3
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Zhao S, Li Y, Chen G, Wang X, Chen N, Wu X. Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection. Genome Res 2023; 33:1958-1974. [PMID: 37871969 PMCID: PMC10760458 DOI: 10.1101/gr.277931.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Abstract
As influential regulatory elements in the genome, enhancers control gene expression under specific cellular conditions, and such connections are dynamic under different conditions. However, because of the lack of a genome-wide enhancer-gene connection map, the roles and regulatory pattern of enhancers were poorly investigated in insects, and the dynamic changes of enhancer contacts and functions under different conditions remain elusive. Here, combining Hi-C, ATAC-seq, and H3K27ac ChIP-seq data, we generate the genome-wide enhancer-gene map of silkworm and identify super-enhancers with a role in regulating the expression of vital genes related to cell state maintenance through a sophisticated interaction network. Additionally, a radical attenuation of chromatin interactions is found after infection of Bombyx mori nucleopolyhedrovirus (BmNPV), the main pathogen of silkworm, which directly rearranges the enhancer contacts. Such a rearrangement disturbs the intrinsic enhancer-gene connections in several antiviral genes, resulting in reduced expression of these genes, which accelerates viral infection. Overall, our results reveal the regulatory role of super-enhancers and shed new light on the mechanisms and dynamic changes of the genome-wide enhancer regulatory network.
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Affiliation(s)
- Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Yuedong Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Guanping Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Xingyang Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Nan Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China;
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
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Xia J, Fei S, Wu H, Yang Y, Yu W, Zhang M, Guo Y, Swevers L, Sun J, Feng M. The piRNA pathway is required for nucleopolyhedrovirus replication in Lepidoptera. INSECT SCIENCE 2023; 30:1378-1392. [PMID: 36495071 DOI: 10.1111/1744-7917.13160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The Piwi-interacting RNA (piRNA) pathway has been shown to be involved in the antiviral defense against RNA viruses, especially in mosquitoes, but its universality has been questioned. Here, we used the Bombyx mori nucleopolyhedrovirus (BmNPV) -infected silkworm as a model to explore the effects of the key factors of piRNA pathway, BmAgo3 and Siwi, on replication of a large DNA virus (belonging to the family of Baculoviridae). We demonstrated that BmAgo3 and Siwi could promote the replication of BmNPV through both overexpression and knockdown experiments in BmN cell lines and silkworm larvae. In addition, we also studied the effect of PIWI-class genes on Autographa californica nucleopolyhedrovirus (AcMNPV) replication in the Spodoptera frugiperda cell line Sf9. By knocking down the expression of PIWI-class genes in Sf9, we found that Piwi-like-1 and Piwi-like-2-3 could inhibit AcMNPV replication, while Piwi-like-4-5 promoted virus replication. Our study provides compelling evidence that the piRNA pathway affects host infection by exogenous viruses in Lepidoptera. Also, our results reflect the diversity of the roles of PIWI-class genes in virus infection of the host across species. This study is the first to explore the interaction of PIWI-class proteins with DNA viruses, providing new insights into the functional roles of the piRNA pathway.
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Affiliation(s)
- Junming Xia
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shigang Fei
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hongyun Wu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yifan Yang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wensheng Yu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Mengmeng Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yiyao Guo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, National Center for Scientific Research Demokritos, Institute of Biosciences and Applications, Athens, Greece
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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5
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Santos D, Feng M, Kolliopoulou A, Taning CNT, Sun J, Swevers L. What Are the Functional Roles of Piwi Proteins and piRNAs in Insects? INSECTS 2023; 14:insects14020187. [PMID: 36835756 PMCID: PMC9962485 DOI: 10.3390/insects14020187] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/01/2023]
Abstract
Research on Piwi proteins and piRNAs in insects has focused on three experimental models: oogenesis and spermatogenesis in Drosophila melanogaster, the antiviral response in Aedes mosquitoes and the molecular analysis of primary and secondary piRNA biogenesis in Bombyx mori-derived BmN4 cells. Significant unique and complementary information has been acquired and has led to a greater appreciation of the complexity of piRNA biogenesis and Piwi protein function. Studies performed in other insect species are emerging and promise to add to the current state of the art on the roles of piRNAs and Piwi proteins. Although the primary role of the piRNA pathway is genome defense against transposons, particularly in the germline, recent findings also indicate an expansion of its functions. In this review, an extensive overview is presented of the knowledge of the piRNA pathway that so far has accumulated in insects. Following a presentation of the three major models, data from other insects were also discussed. Finally, the mechanisms for the expansion of the function of the piRNA pathway from transposon control to gene regulation were considered.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
| | - Clauvis N. T. Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
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6
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Hu Z, Zhu F, Chen K. The Mechanisms of Silkworm Resistance to the Baculovirus and Antiviral Breeding. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:381-399. [PMID: 36689303 DOI: 10.1146/annurev-ento-120220-112317] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Silkworm (Bombyx mori) is not only an economic insect but also a model organism for life science research. Bombyx mori nucleopolyhedrovirus (BmNPV) disease is a major infectious disease in the world's sericulture industry. The cocoon loss caused by this disease accounts for more than 60% of the total loss caused by all silkworm diseases. To date, there has been no effective solution for preventing and treating this disease. The most effective measure is to breed disease-resistant varieties. The quickest way to breed disease-resistant varieties is to apply genetic modification. However, this requires that we obtain disease resistance genes and know the mechanism of disease resistance. Since the discovery of disease-resistant resources in 1989, scholars in the sericulture industry around the world have been inspired to search for resistance genes. In the past two decades, with the help of multi-omics technologies, screening of resistance genes, gene localization, protein modification, virus-host interactions, etc., researchers have found some candidate genes that have been proposed to function at the cellular or individual level. Several disease-resistant varieties have been obtained and used in production through hybrid breeding, RNA interference, and genetic modification. This article summarizes and reviews the discovery of and research advances related to silkworm resistance to BmNPV. It is anticipated that the review will inspire scientific researchers to continue searching for disease resistance genes, clarify the molecular mechanism of silkworm disease resistance, and promote disease-resistant silkworm breeding.
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Affiliation(s)
- Zhaoyang Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, China;
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, China;
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China;
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7
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Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
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Actin Contributes to the Hyperexpression of Baculovirus Polyhedrin (polh) and p10 as a Component of Transcription Initiation Complex (TIC). Viruses 2022; 14:v14010153. [PMID: 35062357 PMCID: PMC8779803 DOI: 10.3390/v14010153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/30/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Hyperexpression of polh and p10, two very late genes, is one of the remarkable characteristics in the baculovirus life cycle. However, the mechanisms underlying the hyperexpression of these two genes are still incompletely understood. In this study, actin was identified as a highly potential binding partner of polh and p10 promoters by conducting DNA pull-down and LC–MS/MS analyses. Inhibiting actin dynamics delayed and decreased the transcription of polh and p10. Actin interacted with viral RNA polymerase and transcription regulators, and the nuclear import of viral polymerase was inhibited with the disruption of actin dynamics. Simultaneously, the high enrichment of actin in polh and p10 promoters discovered via a chromatin immunoprecipitation (ChIP) assay indicated that actin was a component of the viral polymerase TIC. Moreover, overexpression of actin surprisingly upregulated the expression of luciferase (Luc) under the control of polh and p10 promoters. Taken together, actin participated in the hyperexpression of polh and p10 as a component of TIC. These results facilitate the promotion of the expression efficiency of foreign genes in the baculovirus expression vector system (BEVS).
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9
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Mattola S, Hakanen S, Salminen S, Aho V, Mäntylä E, Ihalainen TO, Kann M, Vihinen-Ranta M. Concepts to Reveal Parvovirus-Nucleus Interactions. Viruses 2021; 13:1306. [PMID: 34372512 PMCID: PMC8310053 DOI: 10.3390/v13071306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 01/23/2023] Open
Abstract
Parvoviruses are small single-stranded (ss) DNA viruses, which replicate in the nucleoplasm and affect both the structure and function of the nucleus. The nuclear stage of the parvovirus life cycle starts at the nuclear entry of incoming capsids and culminates in the successful passage of progeny capsids out of the nucleus. In this review, we will present past, current, and future microscopy and biochemical techniques and demonstrate their potential in revealing the dynamics and molecular interactions in the intranuclear processes of parvovirus infection. In particular, a number of advanced techniques will be presented for the detection of infection-induced changes, such as DNA modification and damage, as well as protein-chromatin interactions.
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Affiliation(s)
- Salla Mattola
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Satu Hakanen
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Sami Salminen
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Vesa Aho
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
| | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (E.M.); (T.O.I.)
| | - Teemu O. Ihalainen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (E.M.); (T.O.I.)
| | - Michael Kann
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden;
- Department of Clinical Microbiology, Sahlgrenska University Hospital, 41345 Gothenburg, Sweden
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science, University of Jyvaskyla, 40500 Jyvaskyla, Finland; (S.M.); (S.H.); (S.S.); (V.A.)
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10
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H3K4me3 histone modification in baculovirus-infected silkworm cells. Virus Genes 2021; 57:459-463. [PMID: 34185196 DOI: 10.1007/s11262-021-01858-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
Baculovirus infection modulates the chromatin states and gene expression of host insect cells. Here we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of H3 trimethylated at Lys4 (H3K4me3) histone modification in Bombyx mori nucleopolyhedrovirus-infected Bombyx mori cells. The ChIP-seq data revealed the changes of the genome-wide distribution and accumulation of euchromatic histone marks in host insect cells during the progression of baculovirus infection.
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11
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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