Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs
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{"title"=>"Identification and characterization of Cyprinid herpesvirus-3 (CyHV-3) encoded MicroRNAs", "type"=>"journal", "authors"=>[{"first_name"=>"Owen H.", "last_name"=>"Donohoe", "scopus_author_id"=>"57112706100"}, {"first_name"=>"Kathy", "last_name"=>"Henshilwood", "scopus_author_id"=>"6602256857"}, {"first_name"=>"Keith", "last_name"=>"Way", "scopus_author_id"=>"56284623400"}, {"first_name"=>"Roya", "last_name"=>"Hakimjavadi", "scopus_author_id"=>"56097662100"}, {"first_name"=>"David M.", "last_name"=>"Stone", "scopus_author_id"=>"56255953500"}, {"first_name"=>"Dermot", "last_name"=>"Walls", "scopus_author_id"=>"7005011425"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84957922934", "pmid"=>"25928140", "pui"=>"608141929", "isbn"=>"19326203 (ISSN)", "scopus"=>"2-s2.0-84957922934", "doi"=>"10.1371/journal.pone.0125434", "issn"=>"19326203"}, "id"=>"ef095aaa-8004-306e-ac7d-142b3ce16ccc", "abstract"=>"MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA-offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.", "link"=>"http://www.mendeley.com/research/identification-characterization-cyprinid-herpesvirus3-cyhv3-encoded-micrornas", "reader_count"=>19, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>4, "Neuroscience"=>1, "Veterinary Science and Veterinary Medicine"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2047054"], "description"=>"<p>The numbers underneath each graph indicate days post-infection (d.p.i.) with the CyHV-3 N076 isolate. UC denotes uninfected cells. <b>(A)</b> Detection of CyHV-3 genomic DNA by PCR; levels were normalized to CCB cell genomic DNA in each case. <b>(B)</b> Relative levels of the dominant miRNAs from six high probability CyHV-3 pre-miRNAs over the course of the experiment shown in (A) as measured by stem-loop RT-qPCR and normalized to levels of the host miRNA ccr-let-7a.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1399998, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g006", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CyHV_3_miRNAs_are_consistently_expressed_during_in_vitro_infection_of_CCB_cells_/1399998", "title"=>"CyHV-3 miRNAs are consistently expressed during <i>in vitro</i> infection of CCB cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047051"], "description"=>"<p>Total RNA was prepared from CCB cells following an <i>in vitro</i> lytic infection with the CyHV-3 N076 isolate (+) and from uninfected control cells (-). Replicate blots were probed separately for MR5057-miR-3p (left), and the host miRNA ccr-let-7a-5p which served as a loading control (right). The location of size markers (in nucleotides) is indicated on the left; black arrows point to bands corresponding to MR5057-miR-3p and ccr-let-7a-5p (both 22 nt); the open arrow points to the band corresponding to the MR5057 pre-miRNA (56 nt).</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1399995, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_CyHV_3_miRNA_MR5057_miR_3p_and_its_pre_miRNA_by_Northern_blotting_/1399995", "title"=>"Detection of CyHV-3 miRNA MR5057-miR-3p and its pre-miRNA by Northern blotting.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047068", "https://ndownloader.figshare.com/files/2047069"], "description"=>"<div><p>MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (<i>Cyprinus carpio carpio</i>) and koi (<i>Cyprinus carpio koi</i>) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from <i>in vitro</i> CyHV-3 infections led to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection <i>in vitro</i>. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the <i>Alloherpesviridae</i> family, a group distantly related to the <i>Herpesviridae</i> family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.</p></div>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1400012, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0125434.s001", "https://dx.doi.org/10.1371/journal.pone.0125434.s002"], "stats"=>{"downloads"=>0, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_and_Characterization_of_Cyprinid_Herpesvirus_3_CyHV_3_Encoded_MicroRNAs_/1400012", "title"=>"Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047065"], "description"=>"<p><b>(A)</b> Western blot showing relative CyHV-3 rdUTPase levels (top panel) produced 48 h following transfection of CCB cells with pCyHV-3-rdUTPase in combination with miRNA mimics (as indicated above the image). Endogenous β-actin levels are also shown from the same blot (lower panel). <b>(B)</b> Luciferase assays showing relative values obtained from pLS-123-3′ UTR (containing predicted target seed region 5′GCAATT3′) and matched control pLS-123-3′ UTRmut (seed changed to 5′CGTACA3′) in the presence of miRNA mimics. Data are presented as the Log<sub>2</sub> ratios of luciferase activities of targeting to non-targeting miRNA mimics (i.e. MR5057-miR-3p to negative control). The data shown were compiled from three experiments, values represent means between experiments and error bars represent standard deviations; *indicates p < 0.05.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1400009, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g012", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MR5057_miR_3p_interacts_with_the_3_UTR_of_CyHV_3_ORF123_and_downregulates_its_encoded_protein_/1400009", "title"=>"MR5057-miR-3p interacts with the 3′ UTR of CyHV-3 <i>ORF123</i> and downregulates its encoded protein.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047050"], "description"=>"<p>(A) Small RNA deep sequencing read counts and (B) DNA microarray miRNA probe hybridization signal intensities corrected and expressed as multiples of background (MOB). Data from both (A) and (B) were obtained using size-selected miRNA-inclusive RNA (F1 fraction; 17–25 nt) from the same <i>in vitro</i> infection (CyHV-3 H361 isolate). No corresponding hybridization signals were detected in miRNA non-inclusive RNA (F2 faction; 26–35 nt) from the same infection or in miRNA inclusive RNA (F3 fraction, 17–25 nt) from non-infected cells (Dataset S in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125434#pone.0125434.s002\" target=\"_blank\">S1 File</a>). Error bars represent the data range.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1399994, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g003", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_levels_of_miRNAs_derived_from_CyHV_3_pre_miRNA_candidates_MR5057_and_MD11776_/1399994", "title"=>"Comparison of the levels of miRNAs derived from CyHV-3 pre-miRNA candidates MR5057 and MD11776.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047063"], "description"=>"<p><b>(A)</b> Base pairing between MR5057-miR-3p and target site in the <i>ORF123</i> 3′ UTR (genomic co-ordinates in brackets). It is a 7mer-m8 site, in line with the nomenclature system outlined elsewhere [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125434#pone.0125434.ref065\" target=\"_blank\">65</a>]. Complementary nucleotides are shown in bold. Seed matches are highlighted in dark grey. An additional nucleotide representing part of the 7mer-m8 target site is underlined. <b>(B)</b> Genomic location of the same site described in (A) (indicated by the light grey arrow and box). It is located in the 3′ UTR of <i>ORF123</i> which itself overlaps with the predicted longer 3′ UTR from <i>ORF122</i>. The black arrow and box show the location of the <i>ORF122/ORF123</i> polyA signal.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1400007, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g011", "stats"=>{"downloads"=>1, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_a_potential_target_for_CyHV_3_MR5057_miR_3p_/1400007", "title"=>"Identification of a potential target for CyHV-3 MR5057-miR-3p.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047045"], "description"=>"<p><b>(A)</b> and <b>(B)</b> The numbers and general genomic locations of low- and high abundance unique viral reads determined following deep sequencing of small RNAs isolated from CyHV-3-infected CCB cells using viral isolates H361 and N076. <b>(C)</b> and <b>(D)</b> Analysis of the combined read counts of low- and high-abundance unique CyHV-3 reads sequenced from both infections.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1399989, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Small_RNA_sequence_reads_derived_from_CyHV_3_during_in_vitro_infection_of_CCB_cells_/1399989", "title"=>"Small RNA sequence reads derived from CyHV-3 during <i>in vitro</i> infection of CCB cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047059"], "description"=>"<p>Genomic locations of <b>(A)</b> CyHV-3 pre-miRNA MD1111 relative to its potential homologue on the CyHV-2 genome and <b>(B)</b> CyHV-3 pre-miRNAs MD11776 and MD11704 relative to their potential homologues on the CyHV-1 and CyHV-2 genomes.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1400003, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g009", "stats"=>{"downloads"=>1, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_CyHV_3_pre_miRNA_homologues_on_the_genomes_of_CyHV_1_and_2_/1400003", "title"=>"Identification of CyHV-3 pre-miRNA homologues on the genomes of CyHV-1 and -2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047052"], "description"=>"<p>RNA prepared from CyHV-3-infected CCB cells was analysed for viral miRNA expression by <b>(A)</b> small RNA deep sequencing (read counts), and <b>(B)</b> stem-loop RT-qPCR. In (B), all input cDNA came from a common RT reaction; values shown are based on means of replicates and error bars represent the data range.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1399996, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g005", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_expression_levels_of_the_dominant_miRNAs_from_six_high_probability_CyHV_3_pre_miRNAs_/1399996", "title"=>"Relative expression levels of the dominant miRNAs from six high probability CyHV-3 pre-miRNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047066"], "description"=>"<p>IsomiR end heterogeneity analysis for miRNAs from high-probability CyHV-3 pre-miRNAs.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1400010, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.t004", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_IsomiR_end_heterogeneity_analysis_for_miRNAs_from_high_probability_CyHV_3_pre_miRNAs_/1400010", "title"=>"IsomiR end heterogeneity analysis for miRNAs from high-probability CyHV-3 pre-miRNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047048"], "description"=>"<p><b>(A)</b> Genomic locations of pre-miRNAs; all features on the forward strand are shown in black and those on the reverse strand are in grey. <b>(B)</b> Structures (predicted by VMir) of the high-probability CyHV-3 pre-miRNAs shown in (A). The 5′/3′ arm miRNAs and 5′/3′ arm moRNAs are highlighted in red/yellow and green/purple respectively and represent the dominant reads at these loci in the H361 infection, variants (if any) identified in the N076 infection are given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125434#pone.0125434.t002\" target=\"_blank\">Table 2</a>. MiRNA* reads are indicated with an asterisk. MiRNAs partially overlapping with moRNAs are underlined.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1399992, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_locations_and_structures_of_high_probability_CyHV_3_pre_miRNA_identified_using_a_non_automated_approach_/1399992", "title"=>"Genomic locations and structures of high probability CyHV-3 pre-miRNA identified using a non-automated approach.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047061"], "description"=>"<p>CyHV-1 and CyHV-2 sequences that are underlined represent homologous sequences identified by BLASTN, sequences not underlined (i.e. remainder of input sequences) were subsequently manually inspected for sequence similarity. Nucleotides shaded in grey are conserved in all viruses in the respective alignments and those in dark grey are conserved in 2/3 viruses. <b>(A)</b> MD1111—with the exception of the first 3 nucleotides, the MD1111-miR-5p sequence is fully conserved in CyHV-2; <b>(B)</b> MD11776—the seed (bases 2–7) of MD11776-miR-3p is fully conserved and the remainder of the miRNA is also conserved in all three viruses with the exception of two mismatches; <b>(C)</b> MD11704—the MD11704-miR-5p seed region is fully conserved, the MD11704-miR-3p seed region has one mismatch to each virus.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1400005, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g010", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_CyHV_3_pre_miRNAs_to_candidate_homologues_on_the_CyHV_1_and_CyHV_2_genomes_/1400005", "title"=>"Alignment of CyHV-3 pre-miRNAs to candidate homologues on the CyHV-1 and CyHV-2 genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047057"], "description"=>"<p>Total RNA was extracted from samples of gill tissue taken from both healthy carp and carp with Koi Herpesvirus Associated Disease (KHVD), and were analysed for CyHV-3 miRNAs by stem-loop RT-qPCR. Relative values were normalized to levels of host cell miRNA ccr-let-7a. Assays were done in triplicate, values shown are based on means of replicates and error bars represent the standard deviation.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1400001, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g008", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MiRNAs_MR5057_miR_3p_and_MD11776_miR_3p_are_expressed_in_gill_tissues_from_CyHV_3_infected_carp_/1400001", "title"=>"MiRNAs MR5057-miR-3p and MD11776-miR-3p are expressed in gill tissues from CyHV-3-infected carp.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/2047055"], "description"=>"<p><b>(A)</b> Small RNA deep sequencing read counts obtained following infection of CCB cells with CyHV-3 isolate H361, and <b>(B)</b> stem-loop RT-qPCR analysis of RNA from same <i>in vitro</i> infection. Assays were done in duplicate; values shown are based on the means of replicates (error bars represent the data range). <b>(C)</b> Stem-loop RT-qPCR analysis of total RNA from a second non-synchronous <i>in vitro</i> infection (CyHV-3 N076 isolate). Relative expression levels were normalized to host cell miRNA ccr-let-7a. All results are in agreement that MD1111-miR-5p is the miRNA*.</p>", "links"=>[], "tags"=>["Deep sequencing", "CyHV", "bioinformatic analyses", "host gene expression", "Herpesviridae family", "Alloherpesviridae family", "moRNA genes", "viruses encode", "Cyprinus carpio koi", "RNA fractions", "mass mortalities", "DNA microarray hybridization analysis", "mirna", "Cyprinus carpio carpio", "gill tissue", "Cyprinid herpesvirus 3", "Candidate homologues"], "article_id"=>1399999, "categories"=>["Biological Sciences"], "users"=>["Owen H. Donohoe", "Kathy Henshilwood", "Keith Way", "Roya Hakimjavadi", "David M. Stone", "Dermot Walls"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0125434.g007", "stats"=>{"downloads"=>8, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_levels_of_miRNAs_from_both_arms_of_CyHV_3_pre_miRNA_MD1111_/1399999", "title"=>"Relative levels of miRNAs from both arms of CyHV-3 pre-miRNA MD1111.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-30 04:05:13"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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