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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Liu S, Ma X, Wang Z, Lin F, Li M, Li Y, Yang L, Rushdi HE, Riaz H, Gao T, Yang L, Fu T, Deng T. MAEL gene contributes to bovine testicular development through the m5C-mediated splicing. iScience 2023; 26:105941. [PMID: 36711243 PMCID: PMC9876746 DOI: 10.1016/j.isci.2023.105941] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/01/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Knowledge of RNA molecules regulating testicular development and spermatogenesis in bulls is essential for elite bull selection and an ideal breeding program. Herein, we performed direct RNA sequencing (DRS) to explore the functional characterization of RNA molecules produced in the testicles of 9 healthy Simmental bulls at three testicular development stages (prepuberty, puberty, and postpuberty). We identified 5,043 differentially expressed genes associated with testicular weight. These genes exhibited more alternative splicing at sexual maturity, particularly alternative 3' (A3) and 5' (A5) splice sites usage and exon skipping (SE). The expression of hub genes in testicular developmental stages was also affected by both m6A and m5C RNA modifications. We found m5C-mediated splicing events significantly (p < 0.05) increased MAEL gene expression at the isoform level, likely promoting spermatogenesis. Our findings highlight the complexity of RNA processing and expression as well as the regulation of transcripts involved in testicular development and spermatogenesis.
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Affiliation(s)
- Shenhe Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Zichen Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Feng Lin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yali Li
- Wuhan Benagen Technology Co, Ltd, Wuhan 430000, China
| | - Liu Yang
- Wuhan Benagen Technology Co, Ltd, Wuhan 430000, China
| | - Hossam E. Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Hasan Riaz
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Punjab, Pakistan
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Liguo Yang
- China Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China,Corresponding author
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China,Corresponding author
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Mackie J, Kinoti WM, Chahal SI, Lovelock DA, Campbell PR, Tran-Nguyen LTT, Rodoni BC, Constable FE. Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:2716. [PMID: 36297740 PMCID: PMC9607580 DOI: 10.3390/plants11202716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Rapid and reliable detection tools are essential for disease surveillance and outbreak management, and genomic data is essential to determining pathogen origin and monitoring of transmission pathways. Low virus copy number and poor RNA quality can present challenges for genomic sequencing of plant viruses, but this can be overcome by enrichment of target nucleic acid. A targeted whole genome sequencing (TWG-Seq) approach for the detection of cucumber green mottle mosaic virus (CGMMV) has been developed where overlapping amplicons generated using two multiplex RT-PCR assays are then sequenced using the Oxford Nanopore MinION. Near complete coding region sequences were assembled with ≥100× coverage for infected leaf tissue dilution samples with RT-qPCR cycle quantification (Cq) values from 11.8 to 38 and in seed dilution samples with Cq values 13.8 to 27. Consensus sequences assembled using this approach showed greater than 99% nucleotide similarity when compared to genomes produced using metagenomic sequencing. CGMMV could be confidently detected in historical seed isolates with degraded RNA. Whilst limited access to, and costs associated with second-generation sequencing platforms can influence diagnostic outputs, the portable Nanopore technology offers an affordable high throughput sequencing alternative when combined with TWG-Seq for low copy or degraded samples.
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Affiliation(s)
- Joanne Mackie
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Melbourne, VIC 3083, Australia
| | - Wycliff M. Kinoti
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
| | - Sumit I. Chahal
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
| | - David A. Lovelock
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
| | - Paul R. Campbell
- Horticulture and Forestry Science, Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD 4102, Australia
| | | | - Brendan C. Rodoni
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Melbourne, VIC 3083, Australia
| | - Fiona E. Constable
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Melbourne, VIC 3083, Australia
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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Liver biopsy of chronic hepatitis B patients indicates HBV integration profile may complicate the endpoint and effect of entecavir treatment. Antiviral Res 2022; 204:105363. [PMID: 35709897 DOI: 10.1016/j.antiviral.2022.105363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022]
Abstract
AIMS Viral integration profiles attract increased interest in the study of HBV-related hepatocellular carcinoma (HCC), but their features in the early stage of infection and changes due to antiviral treatments remain largely unknown. METHODS Liver biopsies and paired blood samples were obtained from HBeAg-positive patients before and after 48 weeks of entecavir treatment, and a probe-based capture strategy was applied for analyzing the HBV integrations in these samples. Serum HBV markers, including viral DNA, pgRNA, and HBsAg, were longitudinally assessed. RESULTS Entecavir treatment successfully reduced the levels of ALT, AST, and HBV serological markers (HBeAg, HBV pgRNA, and HBV DNA) in all patients (<40 years old). As expected, HBV integrations contributed to HBsAg production, with the total number of integrations positively correlated with serum HBsAg level (r = 0.47, P = 0.04). Along with repressed HBV replication, the number of viral integrations in liver biopsies decreased by about 1.94-fold after ETV treatment, with viral breakpoints significantly enriched within nt 1600-1900 of the HBV genome. No recurrent events were observed both at baseline and after treatment for the same individual, and only one same integration was found in two patients. Unlike in tumors, integrations in CHB biopsies seemed to have no chromosomal preference. Moreover, CHB integrations demonstrated lower enrichment scores for open active states than tumors, such as DNase, TssA, and ZNF/Rpts, and the scores reduced after ETV treatment. The antiviral therapy led to the disappearance of the enrichment tendency of integrations in both open chromatin and heterochromatin regions. CONCLUSION Reduced HBV replications by the nucleoside analogue may lead to decreased viral integrations in the liver, and those contributing to the HBsAg production may consistently occur. The pattern of HBV integration after ETV treatment is more random and irregular, which may contribute to a reduced risk of liver cancer due to antiviral treatment.
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Huang M, Jiang Y, Qin R, Jiang D, Chang D, Tian Z, Li C, Wang C. Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response. FRONTIERS IN PLANT SCIENCE 2022; 13:866322. [PMID: 35665156 PMCID: PMC9158574 DOI: 10.3389/fpls.2022.866322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/22/2022] [Indexed: 06/04/2023]
Abstract
Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant-pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein-protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN-soybean interaction mechanism as a model will present more understanding of other plant-nematode interactions.
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Affiliation(s)
- Minghui Huang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Ye Jiang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Ruifeng Qin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Dan Jiang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Doudou Chang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Zhongyan Tian
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Chunjie Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Congli Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Wang X, Stevens KC, Ting JM, Marras AE, Rezvan G, Wei X, Taheri-Qazvini N, Tirrell MV, Liu C. Translocation Behaviors of Synthetic Polyelectrolytes through Alpha-Hemolysin (α-HL) and Mycobacterium smegmatis Porin A (MspA) Nanopores. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2022; 169:057510. [PMID: 35599744 PMCID: PMC9121822 DOI: 10.1149/1945-7111/ac6c55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNAs have been used as probes for nanopore sensing of noncharged biomacromolecules due to its negative phosphate backbone. Inspired by this, we explored the potential of diblock synthetic polyelectrolytes as more flexible and inexpensive nanopore sensing probes by investigating translocation behaviors of PEO-b-PSS and PEO-b-PVBTMA through commonly used alpha-hemolysin (α-HL) and Mycobacterium smegmatis porin A (MspA) nanopores. Translocation recordings in different configurations of pore orientation and testing voltage indicated efficient PEO-b-PSS translocations through α-HL and PEO-b-PVBTMA translocations through MspA. This work provides insight into synthetic polyelectrolyte-based probes to expand probe selection and flexibility for nanopore sensing.
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Affiliation(s)
- Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Kaden C. Stevens
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jeffrey M. Ting
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander E. Marras
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Gelareh Rezvan
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Nader Taheri-Qazvini
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew V. Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
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Wang Z, Wang R, Lu Y, An L, Shi AC, Wang ZG. Mechanisms of Flow-Induced Polymer Translocation. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Zhenhua Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Ruishu Wang
- Department of Mathematics, Jilin University, Changchun 130012, P. R. China
| | - Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - An-Chang Shi
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Abstract
The force- and flow-induced translocation processes of linear and ring polymers are studied using a combination of multiparticle collision dynamics and molecular dynamics, focusing on the behavior of the polymer translocation time. We compare the force- and flow-induced translocations of linear and ring polymers. It is found that when the translocation time (τ*) is characterized by scaling exponents, δ, δ', and α, via the relations τ* ∼ fδNα and τ* ∼ Jδ'Nα, the scaling exponents are not constants. For long chains tested, α = 1.0 for both force- and flow-induced translocations. The difference between the force- and flow-induced translocations stems from different monomer crowding effects due to distinct flow patterns outside the channel. Furthermore, general relations for polymer translocation time are derived for these two translocation processes, which are in good agreement with the simulation results. Our results provide clear molecular pictures for the force- and flow-induced translocations, which shed light on the understanding of translocation dynamics and provide guidance for practical applications such as molecular sequencing and ultrafiltration.
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Affiliation(s)
- Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Zhenhua Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - An-Chang Shi
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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Zhang D, Guo S, Schrodi SJ. Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties. Int J Mol Sci 2021; 22:9858. [PMID: 34576022 PMCID: PMC8466338 DOI: 10.3390/ijms22189858] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV), the well-studied oncovirus that contributes to the majority of hepatocellular carcinomas (HCC) worldwide, can cause a severe inflammatory microenvironment leading to genetic and epigenetic changes in hepatocyte clones. HBV replication contributes to the regulation of DNA methyltransferase gene expression, particularly by X protein (HBx), and subsequent methylation changes may lead to abnormal transcription activation of adjacent genes and genomic instability. Undoubtedly, the altered expression of these genes has been known to cause diverse aspects of infected hepatocytes, including apoptosis, proliferation, reactive oxygen species (ROS) accumulation, and immune responses. Additionally, pollutant-induced DNA methylation changes and aberrant methylation of imprinted genes in hepatocytes also complicate the process of tumorigenesis. Meanwhile, hepatocytes also contribute to epigenetic modification of the viral genome to affect HBV replication or viral protein production. Meanwhile, methylation levels of HBV integrants and surrounding host regions also play crucial roles in their ability to produce viral proteins in affected hepatocytes. Both host and viral changes can provide novel insights into tumorigenesis, individualized responses to therapeutic intervention, disease progress, and early diagnosis. As such, DNA methylation-mediated epigenetic silencing of cancer-related genes and viral replication is a compelling therapeutic goal to reduce morbidity and mortality from liver cancer caused by chronic HBV infection. In this review, we summarize the most recent research on aberrant DNA methylation associated with HBV infection, which is involved in HCC development, and provide an outlook on the future direction of the research.
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Affiliation(s)
- Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Steven J. Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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