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{"title"=>"Characterization of the host factors required for hepadnavirus covalently closed circular (ccc) DNA formation", "type"=>"journal", "authors"=>[{"first_name"=>"Haitao", "last_name"=>"Guo", "scopus_author_id"=>"55468649000"}, {"first_name"=>"Chunxiao", "last_name"=>"Xu", "scopus_author_id"=>"55725645900"}, {"first_name"=>"Tianlun", "last_name"=>"Zhou", "scopus_author_id"=>"7402989470"}, {"first_name"=>"Timothy M.", "last_name"=>"Block", "scopus_author_id"=>"7102759116"}, {"first_name"=>"Ju Tao", "last_name"=>"Guo", "scopus_author_id"=>"7404490091"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"365445235", "doi"=>"10.1371/journal.pone.0043270", "pmid"=>"22912842", "issn"=>"19326203", "scopus"=>"2-s2.0-84865060138", "sgr"=>"84865060138"}, "id"=>"8d38d3bd-8c1d-3a11-8fee-0c048423d05c", "abstract"=>"Synthesis of the covalently closed circular (ccc) DNA is a critical, but not well-understood step in the life cycle of hepadnaviruses. Our previous studies favor a model that removal of genome-linked viral DNA polymerase occurs in the cytoplasm and the resulting deproteinized relaxed circular DNA (DP-rcDNA) is subsequently transported into the nucleus and converted into cccDNA. In support of this model, our current study showed that deproteinization of viral double-stranded linear (dsl) DNA also took place in the cytoplasm. Furthermore, we demonstrated that Ku80, a component of non-homologous end joining DNA repair pathway, was essential for synthesis of cccDNA from dslDNA, but not rcDNA. In an attempt to identify additional host factors regulating cccDNA biosynthesis, we found that the DP-rcDNA was produced in all tested cell lines that supported DHBV DNA replication, but cccDNA was only synthesized in the cell lines that accumulated high levels of DP-rcDNA, except for NCI-H322M and MDBK cells, which failed to synthesize cccDNA despite of the existence of nuclear DP-rcDNA. The results thus imply that while removal of the genome-linked viral DNA polymerase is most likely catalyzed by viral or ubiquitous host function(s), nuclear factors required for the conversion of DP-rcDNA into cccDNA and/or its maintenance are deficient in the above two cell lines, which could be useful tools for identification of the elusive host factors essential for cccDNA biosynthesis or maintenance.", "link"=>"http://www.mendeley.com/research/characterization-host-factors-required-hepadnavirus-covalently-closed-circular-ccc-dna-formation", "reader_count"=>25, "reader_count_by_academic_status"=>{"Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>7, "Student > Bachelor"=>1, "Professor"=>1, "Other"=>1}, "reader_count_by_user_role"=>{"Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>7, "Student > Bachelor"=>1, "Professor"=>1, "Other"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>17, "Medicine and Dentistry"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Colombia"=>2, "Venezuela"=>1, "United States"=>1}, "group_count"=>1}

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• http://doi.org/10.1016/j.drudis.2015.01.008
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• http://doi.org/10.1016/j.antiviral.2016.08.026

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• {"id"=>"235121674268323841", "text"=>"Characterization of the Host Factors Required for Hepadnavirus Covalently Closed Circular (ccc) DNA Formation: b... http://t.co/E5fKcWgc", "created_at"=>"2012-08-13T21:12:30Z", "user"=>"Sequilabs", "user_name"=>"Sequilab", "user_profile_image"=>"http://a0.twimg.com/profile_images/1159879909/SeqBrand_normal.jpg"}
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• {"files"=>["https://ndownloader.figshare.com/files/593812"], "description"=>"<p>Note: <i>^a</i> each “<b>+</b>” represents one quarter of quantitative signal for each DHBV DNA species from HepG2 cells by DNA hybridization; <i>^b</i> undetectable by DNA hybridization; <i>^c</i> not determined due to cell death after AdDHBV1S infection.</p>", "links"=>[], "tags"=>["permissiveness", "dhbv", "deproteinization", "cccdna"], "article_id"=>264301, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.t001", "stats"=>{"downloads"=>5, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cell_Permissiveness_on_DHBV_replication_deproteinization_and_cccDNA_formation_/264301", "title"=>"Cell Permissiveness on DHBV replication, deproteinization and cccDNA formation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:01:44"}
• {"files"=>["https://ndownloader.figshare.com/files/593635"], "description"=>"<p>See text for detailed explanation.</p>", "links"=>[], "tags"=>["cccdna", "biosynthesis", "pathways", "rc"], "article_id"=>264126, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.g007", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_cccDNA_biosynthesis_pathways_from_rc_and_dslDNA_/264126", "title"=>"Schematic representation of cccDNA biosynthesis pathways from rc and dslDNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 01:00:45"}
• {"files"=>["https://ndownloader.figshare.com/files/593534"], "description"=>"<p>(<b>A</b>) AML12 and MDBK were infected with AdDHBV1S at a MOI of 10. On day 5 post infection, DHBV core-associated (upper panel) and Hirt DNA (lower panel) were extracted and analyzed by Southern blot hybridization. Hirt DNA prepared from the cytoplasmic and nuclear fractions of AdDHBV1S-infecetd AML12 and MDBK cells (B) or NCI-H322M cells (C) were analyzed by Southern blot hybridization assay. Core or Hirt DNA extracted from dstet5 cells cultured in the absence of tetracycline for 8 days (lane 1) and unit length of linear DHBV DNA (lane 2) served as controls.</p>", "links"=>[], "tags"=>["dp-dna", "mdbk", "nci-h322m"], "article_id"=>264021, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.g006", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Subcellular_distribution_of_the_DP_DNA_in_MDBK_and_NCI_H322M_cells_/264021", "title"=>"Subcellular distribution of the DP-DNA in MDBK and NCI-H322M cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 01:00:10"}
• {"files"=>["https://ndownloader.figshare.com/files/592933"], "description"=>"<p>(A) DSL212 cells were cultured in the absence of tetracycline for 6 days. Cytoplasm and nuclei were fractionated with QIAgen Qproteome Cell Compartment Kit by following the manufacturer's directions. DHBV core-associated DNA and Hirt DNA were extracted from whole cell, cytoplasm and nuclear fractions were analyzed by Southern blot assay. (B) DHBV core-associated DNA and Hirt DNA were extracted from whole cell, cytoplasm and nuclear fractions of HepG3 cells (a HepG2-derived stable cell line containing an integrated DHBV head-to-tail unit-length DNA dimer) were analyzed by Southern blot assay.</p>", "links"=>[], "tags"=>["dhbv", "dna", "replication", "intermediates", "hepg2"], "article_id"=>263426, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.g002", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Subcellular_distribution_of_DHBV_DNA_replication_intermediates_in_HepG2_cells_/263426", "title"=>"Subcellular distribution of DHBV DNA replication intermediates in HepG2 cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 00:57:03"}
• {"files"=>["https://ndownloader.figshare.com/files/593068"], "description"=>"<p>Cell lines used in this experiment are CHO-K1 and its derived cell line Xrs-5 harboring defective gene of the p86 subunit of the Ku autoantigen, four human fibroblast cell lines GM16133, GM16135, GM16147 and GM16089 that are defective in XRCC1, the catalytic subunit of DNA-PK, XRCC4 and ligase IV, respectively. The cells are infected with AdDHBV1S at a MOI of 10 and infected cells are harvested on day 3 post infection. DHBV core-associated (upper panel) and Hirt DNA (lower panel) were extracted and analyzed by Southern blot hybridization.</p>", "links"=>[], "tags"=>["dna", "replication", "cccdna", "cells", "lines", "defective", "nhej"], "article_id"=>263548, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.g003", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DHBV_DNA_replication_and_cccDNA_formation_in_a_panel_of_cells_lines_that_are_defective_in_NHEJ_DNA_repair_pathway_/263548", "title"=>"DHBV DNA replication and cccDNA formation in a panel of cells lines that are defective in NHEJ DNA repair pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 00:57:41"}
• {"files"=>["https://ndownloader.figshare.com/files/593211"], "description"=>"<p>(A) CHO-K1 and Xrs-5 cells were transfected with plasmid DHBV-1S or 1Sdsl-3, respectively. On the day five post transfection, the cells were harvested and DHBV core-associated (upper panel) and Hirt DNA (lower panel) were extracted and analyzed by Southern blot hybridization. Unit-length DHBV genomic DNA served as a molecular weight control. (B) Xrs-5 cells were co-transfected with plasmid 1Sdsl-3 and vector plasmid pUC119 (lane 2), plasmid expressing wild-type Ku80 or Ku80-YFP fusion protein, respectively. The cells were harvested on day 5 post transfection. Core (upper panel) and Hirt (middle panel) DNA were detected by Southern blot hybridization. Ku80 and Ku80-YFP expression were detected by Western blot assay (lower panel). β-actin served as a loading control.</p>", "links"=>[], "tags"=>["ku80", "dhbv", "cccdna", "dsldna"], "article_id"=>263703, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.g004", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Role_of_Ku80_in_DHBV_cccDNA_formation_from_dslDNA_precursors_/263703", "title"=>"Role of Ku80 in DHBV cccDNA formation from dslDNA precursors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 00:58:27"}
• {"files"=>["https://ndownloader.figshare.com/files/592771"], "description"=>"<p>DSL212 cells were seeded in 6-well plates and cultured in the presence of tetracycline (1 μg/ml) until cell monolayers became confluent. Cells were then cultured in media without tetracycline and harvested at the indicated days since the removal of tetracycline. Total cellular RNA, cytoplasmic core DNA and total cellular Hirt DNA were extracted and analyzed by Northern and Southern blot hybridization, respectively. (A) For viral RNA analysis, each lane was loaded with 5 μg of total RNA. pgRNA, pregenomic RNA; sRNA, mRNAs specifying the two envelope proteins. Ribosomal RNA (28S and 18S) served as loading controls. For DHBV core DNA (B) and Hirt DNA (C) analysis, each lane represents the amount of viral DNA extracted from one half of cells in a well of 6-well plate. RC, relaxed circular DNA; DSL, double stranded linear DNA; SS. single stranded DNA; cccDNA, covalently-closed circular DNA. Unit length of linear DHBV DNA (lane 10) and core or Hirt DNA extracted from dstet5 cells <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043270#pone.0043270-Guo4\" target=\"_blank\">[40]</a> cultured in the absence of tetracycline for 8 days (lane 11) served as controls.</p>", "links"=>[], "tags"=>["dhbv", "rna", "dna", "replication", "cccdna", "dsl212"], "article_id"=>263254, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.g001", "stats"=>{"downloads"=>3, "page_views"=>89, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kinetics_of_DHBV_RNA_transcription_DNA_replication_and_cccDNA_formation_in_DSL212_cells_/263254", "title"=>"Kinetics of DHBV RNA transcription, DNA replication and cccDNA formation in DSL212 cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 00:56:04"}
• {"files"=>["https://ndownloader.figshare.com/files/593406"], "description"=>"<p>The indicated cell lines were seeded onto 6-well plate and infected with AdDHBV1S at a MOI of 10. Five days post infection, DHBV core-associated (A) and Hirt DNA (B) were extracted and analyzed by Southern blot hybridization. Each lane represents the amount of viral DNA extracted from one half of cells in a well of 6-well plate.</p>", "links"=>[], "tags"=>["dna", "replication", "cccdna", "lines", "infected"], "article_id"=>263894, "categories"=>["Virology", "Biochemistry"], "users"=>["Haitao Guo", "Chunxiao Xu", "Tianlun Zhou", "Timothy M. Block", "Ju-Tao Guo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043270.g005", "stats"=>{"downloads"=>1, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DHBV_DNA_replication_and_cccDNA_formation_in_a_panel_of_human_cell_lines_infected_by_AdDHBV1S_/263894", "title"=>"DHBV DNA replication and cccDNA formation in a panel of human cell lines infected by AdDHBV1S.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 00:59:27"}

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Relative Metric

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F1000Prime