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Wu Z, Wang L, Wang X, Sun Y, Li H, Zhang Z, Ren C, Zhang X, Li S, Lu J, Xu L, Yue X, Hong Y, Li Q, Zhu H, Gong Y, Gao C, Hu H, Gao L, Liang X, Ma C. cccDNA Surrogate MC-HBV-Based Screen Identifies Cohesin Complex as a Novel HBV Restriction Factor. Cell Mol Gastroenterol Hepatol 2022; 14:1177-1198. [PMID: 35987451 PMCID: PMC9579331 DOI: 10.1016/j.jcmgh.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV), existing as a stable minichromosome in the hepatocyte, is responsible for persistent HBV infection. Maintenance and sustained replication of cccDNA require its interaction with both viral and host proteins. However, the cccDNA-interacting host factors that limit HBV replication remain elusive. METHODS Minicircle HBV (MC-HBV), a recombinant cccDNA, was constructed based on chimeric intron and minicircle DNA technology. By mass spectrometry based on pull-down with biotinylated MC-HBV, the cccDNA-hepatocyte interaction profile was mapped. HBV replication was assessed in different cell models that support cccDNA formation. RESULTS MC-HBV supports persistent HBV replication and mimics the cccDNA minichromosome. The MC-HBV-based screen identified cohesin complex as a cccDNA binding host factor, leading to reduced HBV replication. Mechanistically, with the help of CCCTC-binding factor (CTCF), which has specific binding sites on cccDNA, cohesin loads on cccDNA and reshapes cccDNA confirmation to prevent RNA polymerase II enrichment. Interestingly, HBV X protein transcriptionally reduces structural maintenance of chromosomes complex expression to partially relieve the inhibitory role of the cohesin complex on HBV replication. CONCLUSIONS Our data not only provide a feasible approach to explore cccDNA-binding factors, but also identify cohesin/CTCF complex as a critical host restriction factor for cccDNA-driven HBV replication. These findings provide a novel insight into cccDNA-host interaction and targeted therapeutic intervention for HBV infection.
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Affiliation(s)
- Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Liyuan Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xin Wang
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Yang Sun
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Haoran Li
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Zhaoying Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Caiyue Ren
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohui Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Shuangjie Li
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Jinghui Lu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Leiqi Xu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Xuetian Yue
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Yue Hong
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Qiang Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yaoqin Gong
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chengjiang Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Huili Hu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China,Correspondence Address correspondence to: Chunhong Ma, PhD, Key Laboratory for Experimental Teratology of Ministry of Education and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012 China.
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Garrido-Godino AI, Martín-Expósito M, Gutiérrez-Santiago F, Perez-Fernandez J, Navarro F. Rpb4/7, a key element of RNA pol II to coordinate mRNA synthesis in the nucleus with cytoplasmic functions in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194846. [PMID: 35905859 DOI: 10.1016/j.bbagrm.2022.194846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Affiliation(s)
- A I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - M Martín-Expósito
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - F Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - J Perez-Fernandez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain.
| | - F Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain.
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Cavelier G, Anastassiou D. Phenotype analysis using network motifs derived from changes in regulatory network dynamics. Proteins 2005; 60:525-46. [PMID: 15971229 DOI: 10.1002/prot.20538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The intrinsic dynamic response of a transcriptional regulatory network depends directly on molecular interactions in the cellular transcription, translation, and degradation machineries. These interactions can be incorporated into dynamic mathematical models of the biochemical system using the biophysical relationship with the model parameters. Modifications of such interactions bring changes to the biological behavior of the cells, and therefore, many normal and pathological cellular states depend on them. It is important for analysis, prediction, diagnosis, and treatment of cellular function to have an experimentally derived model with parameters that adequately represent the molecular interactions of interest. Finding the model and parameters of a transcriptional regulatory network is a difficult task that has been approached at different levels and with different techniques. We develop here a new analysis method (based on previous work on network inference, modeling, and parameter identification) that finds the most changed parameters from yeast oligonucleotide microarray expression patterns in cases where a phenotype difference exists between two samples. We then relate and examine the changed parameters with their associated genes, corresponding genetic functional categories, and particular subnetworks and connectivities. The biophysical bases for these changes are also identified by studying the relationship of the changed parameters with the transcription, translation, and degradation mechanisms. The method is improved to cases where there are two or more transcription factors influencing transcription, and a statistical analysis is performed to give a measurement of the uniqueness and robustness of the parameter fit.
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Affiliation(s)
- German Cavelier
- Genomic Information Systems Laboratory, Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
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