Genome-Wide Identification of the Target Genes of AP2-O, a Plasmodium AP2-Family Transcription Factor
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"Genome-Wide Identification of the Target Genes of AP2-O, a Plasmodium AP2-Family Transcription Factor", "type"=>"journal", "authors"=>[{"first_name"=>"Izumi", "last_name"=>"Kaneko", "scopus_author_id"=>"15136150700"}, {"first_name"=>"Shiroh", "last_name"=>"Iwanaga", "scopus_author_id"=>"7202370186"}, {"first_name"=>"Tomomi", "last_name"=>"Kato", "scopus_author_id"=>"55483061300"}, {"first_name"=>"Issei", "last_name"=>"Kobayashi", "scopus_author_id"=>"57200896230"}, {"first_name"=>"Masao", "last_name"=>"Yuda", "scopus_author_id"=>"7003492351"}], "year"=>2015, "source"=>"PLoS Pathogens", "identifiers"=>{"scopus"=>"2-s2.0-84930338162", "sgr"=>"84930338162", "issn"=>"15537374", "doi"=>"10.1371/journal.ppat.1004905", "pmid"=>"26018192", "isbn"=>"1553-7366", "pui"=>"604704932"}, "id"=>"692f0079-4bb3-3252-97e7-1a5f3b8014c9", "abstract"=>"Stage-specific transcription is a fundamental biological process in the life cycle of the Plasmodium parasite. Proteins containing the AP2 DNA-binding domain are responsible for stage-specific transcriptional regulation and belong to the only known family of transcription factors in Plasmodium parasites. Comprehensive identification of their target genes will advance our understanding of the molecular basis of stage-specific transcriptional regulation and stage-specific parasite development. AP2-O is an AP2 family transcription factor that is expressed in the mosquito midgut-invading stage, called the ookinete, and is essential for normal morphogenesis of this stage. In this study, we identified the genome-wide target genes of AP2-O by chromatin immunoprecipitation-sequencing and elucidate how this AP2 family transcription factor contributes to the formation of this motile stage. The analysis revealed that AP2-O binds specifically to the upstream genomic regions of more than 500 genes, suggesting that approximately 10% of the parasite genome is directly regulated by AP2-O. These genes are involved in distinct biological processes such as morphogenesis, locomotion, midgut penetration, protection against mosquito immunity and preparation for subsequent oocyst development. This direct and global regulation by AP2-O provides a model for gene regulation in Plasmodium parasites and may explain how these parasites manage to control their complex life cycle using a small number of sequence-specific AP2 transcription factors.", "link"=>"http://www.mendeley.com/research/genomewide-identification-target-genes-ap2o-plasmodium-ap2family-transcription-factor", "reader_count"=>59, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>9, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>9, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>34, "Medicine and Dentistry"=>4, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Social Sciences"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>3, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1}, "group_count"=>3}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/84930338162"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/84930338162?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84930338162&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=84930338162&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/84930338162", "dc:identifier"=>"SCOPUS_ID:84930338162", "eid"=>"2-s2.0-84930338162", "dc:title"=>"Genome-Wide Identification of the Target Genes of AP2-O, a Plasmodium AP2-Family Transcription Factor", "dc:creator"=>"Kaneko I.", "prism:publicationName"=>"PLoS Pathogens", "prism:issn"=>"15537366", "prism:eIssn"=>"15537374", "prism:volume"=>"11", "prism:issueIdentifier"=>"5", "prism:pageRange"=>nil, "prism:coverDate"=>"2015-01-01", "prism:coverDisplayDate"=>"1 May 2015", "prism:doi"=>"10.1371/journal.ppat.1004905", "citedby-count"=>"26", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"Mie University School of Medicine", "affiliation-city"=>"Tsu", "affiliation-country"=>"Japan"}], "pubmed-id"=>"26018192", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e1004905", "source-id"=>"4000151809", "openaccess"=>"1", "openaccessFlag"=>true}

Facebook

  • {"url"=>"http%3A%2F%2Fjournals.plos.org%2Fplospathogens%2Farticle%3Fid%3D10.1371%252Fjournal.ppat.1004905", "share_count"=>1, "like_count"=>0, "comment_count"=>0, "click_count"=>0, "total_count"=>1}

Twitter

Counter

  • {"month"=>"5", "year"=>"2015", "pdf_views"=>"108", "xml_views"=>"4", "html_views"=>"666"}
  • {"month"=>"6", "year"=>"2015", "pdf_views"=>"139", "xml_views"=>"4", "html_views"=>"599"}
  • {"month"=>"7", "year"=>"2015", "pdf_views"=>"46", "xml_views"=>"0", "html_views"=>"165"}
  • {"month"=>"8", "year"=>"2015", "pdf_views"=>"20", "xml_views"=>"0", "html_views"=>"187"}
  • {"month"=>"9", "year"=>"2015", "pdf_views"=>"33", "xml_views"=>"1", "html_views"=>"222"}
  • {"month"=>"10", "year"=>"2015", "pdf_views"=>"19", "xml_views"=>"1", "html_views"=>"173"}
  • {"month"=>"11", "year"=>"2015", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"129"}
  • {"month"=>"12", "year"=>"2015", "pdf_views"=>"16", "xml_views"=>"0", "html_views"=>"79"}
  • {"month"=>"1", "year"=>"2016", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"96"}
  • {"month"=>"2", "year"=>"2016", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"65"}
  • {"month"=>"3", "year"=>"2016", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"62"}
  • {"month"=>"4", "year"=>"2016", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"77"}
  • {"month"=>"5", "year"=>"2016", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"53"}
  • {"month"=>"6", "year"=>"2016", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"44"}
  • {"month"=>"7", "year"=>"2016", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"44"}
  • {"month"=>"8", "year"=>"2016", "pdf_views"=>"16", "xml_views"=>"0", "html_views"=>"61"}
  • {"month"=>"9", "year"=>"2016", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"45"}
  • {"month"=>"10", "year"=>"2016", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"94"}
  • {"month"=>"11", "year"=>"2016", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"30"}
  • {"month"=>"12", "year"=>"2016", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"26"}
  • {"month"=>"1", "year"=>"2017", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"32"}
  • {"month"=>"2", "year"=>"2017", "pdf_views"=>"16", "xml_views"=>"0", "html_views"=>"45"}
  • {"month"=>"3", "year"=>"2017", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"48"}
  • {"month"=>"4", "year"=>"2017", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"33"}
  • {"month"=>"5", "year"=>"2017", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"30"}
  • {"month"=>"6", "year"=>"2017", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"43"}
  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"23", "xml_views"=>"0", "html_views"=>"57"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"31"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"18", "xml_views"=>"1", "html_views"=>"37"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"43"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"32"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"45"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"53"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"17"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"31"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"41"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"25"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"13", "xml_views"=>"3", "html_views"=>"28"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"25"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"37"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"16", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"34"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"24"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"16"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"12", "xml_views"=>"1", "html_views"=>"28"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"19", "xml_views"=>"0", "html_views"=>"40"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"34"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"20"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"20"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"26", "xml_views"=>"0", "html_views"=>"26"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"10", "year"=>"2019", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"16"}
  • {"month"=>"11", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"23"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2084347"], "description"=>"<p>Two independently prepared mutants were used for assessing the phenotype in each gene. The number of oocysts was counted 14 days after an infective blood meal by mosquitoes. The value is an average from 25 mosquitoes. SE, standard error.</p><p>Oocyst formation in mutant parasites.</p>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427625, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004905.t003", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oocyst_formation_in_mutant_parasites_/1427625", "title"=>"Oocyst formation in mutant parasites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-27 02:58:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2084345"], "description"=>"<p>Microarray analysis was performed between wild-type and <i>AP2-O</i>(–) parasites. Genes whose expression was decreased over two-fold are listed. Asterisks indicate genes that have peaks over 1200-bp upstream, in the intron, or in the exon of adjacent genes. Target genes identified in experiment 2 are indicated by “Yes” in the third column.</p><p>List of genes whose expression decreased in <i>AP2-O</i>(–) ookinetes.</p>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427623, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004905.t001", "stats"=>{"downloads"=>7, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_genes_whose_expression_decreased_in_AP2_O_ookinetes_/1427623", "title"=>"List of genes whose expression decreased in <i>AP2-O</i>(–) ookinetes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-27 02:58:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2084346"], "description"=>"<p>RNA-seq analysis was performed in <i>P</i>. <i>berghei</i> ookinetes cultured for 24 h, and genes were ordered according to reads per kilobase of coding sequence per million reads (RPKM) value. Asterisks indicate genes that have peaks over 1200-bp upstream or in the exon of adjacent genes.</p><p>Gene expression analysis of <i>P</i>. <i>berghei</i> ookinetes by RNA-seq.</p>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427624, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004905.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_analysis_of_P_berghei_ookinetes_by_RNA_seq_/1427624", "title"=>"Gene expression analysis of <i>P</i>. <i>berghei</i> ookinetes by RNA-seq.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-27 02:58:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2084344"], "description"=>"<p>A. Overview of the target genes involved in midgut invasion and oocyst formation. B. The numbers of parasites associated with the midgut were compared between wild-type and <i>PPLP4</i>(-) parasites at 24 h after an infective blood meal by mosquitoes, as in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.g003\" target=\"_blank\">Fig 3G</a>. Data are the mean ± SE of three independent experiments using 20 mosquitoes each. C. Ratios of okinetes to total parasites associated with midguts at 24 h after an infective blood meal by mosquitoes. Only ookinetes of fully elongated shape were judged as ookinetes. Data are the mean ± SE of three independent experiments using 20 mosquitoes each. D. Oocysts were counted 2 and 14 dpi. Three independent experiments were performed with each clone. Data are represented as mean ± SE. E. Dot plots of diameters of oocysts at 14 dpi. In total, 200 oocysts were used for measurements in each experiment. Bars represent the mean ± SE of diameters. Mosquitoes were fed on mice infected with <i>POS8</i>(-) parasites constitutively expressing GFP. F. The oocysts in the midgut were counted at different time points (2, 10, and 14 dpi), using the same GFP-expressing parasites as in H. Three independent experiments were performed with each clone. Data are represented as mean ± SE. G. Dot plots of diameters of oocysts at 14 dpi. In total, 200 oocysts were used for measurements in each experiment. Bars represent the mean ± SE of diameters. Mosquitoes were fed on mice infected with <i>CYC3</i>(-) parasites constitutively expressing GFP. H. Fluorescence microscopy image of a mosquito midgut infected with wild-type (left) and <i>CYC3</i>(-) (right) parasites expressing GFP at 14 dpi. Scale bar, 300 μm.</p>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427622, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004905.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Target_genes_required_for_midgut_invasion_and_oocyst_formation_/1427622", "title"=>"Target genes required for midgut invasion and oocyst formation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-27 02:58:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2084329"], "description"=>"<p>A. ChIP-seq experiments were performed independently using two different sequence platforms: an Illumina Genome analyzer and an ABI SOLiD 5500 system. This figure shows AP2-O peaks in each experiment within a 200-kb region (350–550-kb) of the fifth chromosome. The Integrative Genomic Viewer [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.ref056\" target=\"_blank\">56</a>] was used for generating this image from bedgraph files (S ChIP-seq bedgraph). Peak call was performed with the MACS2 program [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.ref057\" target=\"_blank\">57</a>], and 1,540 and 1,111 peaks were identified (FDR < 0.01, fold enrichments > 5). B. Distance of each peak in experiment 2 (1,111 peaks) to the nearest peak in experiment 1 (1,570 peaks) was calculated. Numbers of peaks that have a matching peak within the selected distance were plotted. The graph indicates that nearly 90% of peaks in experiment 2 have counterparts in those in experiment 1. C. Sequences enriched around the summits of AP2-O peaks. Logos were generated using WebLogo 3.3 (<a href=\"http://weblogo.threeplusone.com/create.cgi\" target=\"_blank\">http://weblogo.threeplusone.com/create.cgi</a>) [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.ref058\" target=\"_blank\">58</a>]. D. Distances between the predicted summits of the AP2-O peaks and the motif sequences. The horizontal axis indicates the distance from the summit to the nearest motif sequence (the bin size is 20-bp). The vertical axis indicates the number of peaks in each region (total number of peaks = 959). E. The distribution of AP2-O peaks in the upstream regions of the target genes. The horizontal axis indicates the distance between the summits of the AP2-O peaks and the first methionine codon. The data were obtained from 53 putative target genes identified using microarray analysis. F. The <i>P</i>. <i>berghei</i> genes were divided into six groups containing 1,000 genes each (except for the 6<sup>th</sup> group, which contained 900 genes) according to RPKM values estimated by RNA-seq. The number of target genes in each group is shown as a histogram. The horizontal axis indicates the groups ordered according to their expression levels. G. A pie chart showing the functional categories of target genes (282 genes in total). Hypothetical protein genes are not shown. The number of members in each group is shown on the chart.</p>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427613, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004905.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AP2_O_targets_over_500_genes_in_the_genome_/1427613", "title"=>"AP2-O targets over 500 genes in the genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-27 02:58:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2084369", "https://ndownloader.figshare.com/files/2084370", "https://ndownloader.figshare.com/files/2084371", "https://ndownloader.figshare.com/files/2084372", "https://ndownloader.figshare.com/files/2084373", "https://ndownloader.figshare.com/files/2084374", "https://ndownloader.figshare.com/files/2084375", "https://ndownloader.figshare.com/files/2084376", "https://ndownloader.figshare.com/files/2084377", "https://ndownloader.figshare.com/files/2084378", "https://ndownloader.figshare.com/files/2084379"], "description"=>"<div><p>Stage-specific transcription is a fundamental biological process in the life cycle of the <i>Plasmodium</i> parasite. Proteins containing the AP2 DNA-binding domain are responsible for stage-specific transcriptional regulation and belong to the only known family of transcription factors in <i>Plasmodium</i> parasites. Comprehensive identification of their target genes will advance our understanding of the molecular basis of stage-specific transcriptional regulation and stage-specific parasite development. AP2-O is an AP2 family transcription factor that is expressed in the mosquito midgut-invading stage, called the ookinete, and is essential for normal morphogenesis of this stage. In this study, we identified the genome-wide target genes of AP2-O by chromatin immunoprecipitation-sequencing and elucidate how this AP2 family transcription factor contributes to the formation of this motile stage. The analysis revealed that AP2-O binds specifically to the upstream genomic regions of more than 500 genes, suggesting that approximately 10% of the parasite genome is directly regulated by AP2-O. These genes are involved in distinct biological processes such as morphogenesis, locomotion, midgut penetration, protection against mosquito immunity and preparation for subsequent oocyst development. This direct and global regulation by AP2-O provides a model for gene regulation in <i>Plasmodium</i> parasites and may explain how these parasites manage to control their complex life cycle using a small number of sequence-specific AP2 transcription factors.</p></div>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427641, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1004905.s001", "https://dx.doi.org/10.1371/journal.ppat.1004905.s002", "https://dx.doi.org/10.1371/journal.ppat.1004905.s003", "https://dx.doi.org/10.1371/journal.ppat.1004905.s004", "https://dx.doi.org/10.1371/journal.ppat.1004905.s005", "https://dx.doi.org/10.1371/journal.ppat.1004905.s006", "https://dx.doi.org/10.1371/journal.ppat.1004905.s007", "https://dx.doi.org/10.1371/journal.ppat.1004905.s008", "https://dx.doi.org/10.1371/journal.ppat.1004905.s009", "https://dx.doi.org/10.1371/journal.ppat.1004905.s010", "https://dx.doi.org/10.1371/journal.ppat.1004905.s011"], "stats"=>{"downloads"=>10, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Identification_of_the_Target_Genes_of_AP2_O_a_Plasmodium_AP2_Family_Transcription_Factor/1427641", "title"=>"Genome-Wide Identification of the Target Genes of AP2-O, a <i>Plasmodium</i> AP2-Family Transcription Factor", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-05-27 02:58:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2084343"], "description"=>"<p>A. The pellicle structure and its components are illustrated. Targets are highlighted in red. In addition to the proteins mentioned in the text, targets contained several genes encoding putative pellicular/IMC proteins, viz. apicortin, tubulin-tyrosine ligase (TTL), and small heat shock-related protein 20 (HSP20). Apicortin is involved in the stabilization of microtubules [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.ref059\" target=\"_blank\">59</a>]. TTL, an enzyme adding a tyrosine to the carboxyl end of tubulin, marks the plus ends of growing microtubules and regulates microtubule growth at this site [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.ref060\" target=\"_blank\">60</a>]. HSP20 is involved in ookinete motility [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.ref051\" target=\"_blank\">51</a>,<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004905#ppat.1004905.ref061\" target=\"_blank\">61</a>]. MyoA, myosin A; ADF1, actin-depolymerizing factor 1; SPM, subpellicular microtubule. B. IMC1i was expressed as a GFP-tagged protein using a <i>P</i>. <i>berghei</i> centromere plasmid. Ookinetes were cultured <i>in vitro</i> and observed by fluorescence microscopy at 24 h after fertilization. The apical end of the ookinete is indicated by an arrowhead. Left, merged image of GFP and nuclear staining with Hoechst 33342. Right, optical transmission image. Scale bar, 10 μm. C. Giemsa-stained image of wild-type (left) and <i>IMC1i</i>(-) (right) ookinetes, 24 h after fertilization. Scale bar, 10 μm. D. Fluorescence microscopy image of ookinetes expressing GFP-tagged PUA26. Left, merged image of GFP and nuclear staining with Hoechst 33342. Right, optical transmission image. Scale bar, 10 μm. E. Immunoelectron microscopy image. Cross-sections of two ookinetes expressing GFP-tagged PUA26 are shown. Immunoelectron microscopy was performed with anti-GFP antibodies. Colloidal gold particles (15 nm) are mainly localized at the IMC, which is the layer of high-electron density beneath the plasma membrane. Subpellicular microtubules are indicated by arrowheads. Scale bar, 1 μm. F. Giemsa-stained image of wild-type (left) and <i>PUA26</i>(-) (right) ookinetes at 24 h after fertilization. Scale bar, 10 μm. G. Height—width ratios were compared between wild-type and <i>PUA26</i>(-) ookinetes. Ookinetes were cultured for 24 h and stained with Giemsa. Micrographs were obtained with an Olympus BX60 fluorescence microscope. Height—width ratios of ookinetes were measured with the AquaCosmos software (Hamamatsu Photonic System). In total, 100 ookinetes were analyzed in each parasite population. Bars represent mean ± SE. H. The numbers of parasites associated with the midgut were compared between wild-type and <i>PUA26</i>(-) parasites at 24 h after an infective blood meal by mosquitoes. Data are the mean ± SE of three independent experiments using 20 mosquitoes each. Only parasites on a single side of the midgut were counted.</p>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427621, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004905.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_encoding_pellicular_proteins_are_AP2_O_targets_/1427621", "title"=>"Genes encoding pellicular proteins are AP2-O targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-27 02:58:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2084339"], "description"=>"<p>A. Mapped view of the ChIP-seq and RNA-seq reads of the identified gene in ookinetes. The RNA-seq reads were located in the intergenic region between the 3′-portions of neighboring genes (PBANKA 141090 and PBANKA 141100). The identified ORF is indicated by a red rectangle. B. The amino acid sequences encoded by the corresponding ORFs were aligned in different <i>Plasmodium</i> species. The alignment was performed using ClustalW2.1 (<a href=\"http://www.ebi.ac.uk/Tools/msa/clustalw2\" target=\"_blank\">http://www.ebi.ac.uk/Tools/msa/clustalw2</a>). Pb, <i>P</i>. <i>berghei</i>; Pv. <i>P</i>. <i>vivax</i>; Pf, <i>P</i>. <i>falciparum</i>. C. A fluorescence image of <i>P</i>. <i>berghei</i> ookinetes expressing the GFP-tagged protein. Ookietes were cultured <i>in vitro</i> and observed by fluorescence microscopy at 24 h after fertilization. Apical ends of ookinetes are indicated by arrowheads. Left, merged image of GFP and nuclear staining with Hoechst 33342. Right, optical transmission image. Scale bar, 10 μm. D. Immunoelectron microscopy image of an ookinete expressing the putative protein. Immunoelectron microscopy was performed with anti-GFP antibodies. Left, sagittal section. Colloidal gold particles (15 nm) are located on the apical polar ring, a low-electron density area between the collar (edges of the color are indicated by closed arrowheads) and the striated structure of microtubules (indicated by open arrowheads. Right, cross-section image. Colloidal gold particles (15 nm) are located on the apical polar ring, a low-electron density area between the collar (high-electron density area), and microtubules (cross-sections of microtubules are indicated by arrowheads). The colloidal gold particles are also located on the fibrous tissue observed in the lower-left part of the section, which could be the microtubules adhering to the apical ring and the cytoskeletal fibers surrounding them. Scale bars, 0.5 μm.</p>", "links"=>[], "tags"=>["Plasmodium parasites", "life cycle", "gene", "AP 2 family transcription factor", "regulation"], "article_id"=>1427617, "categories"=>["Biological Sciences"], "users"=>["Izumi Kaneko", "Shiroh Iwanaga", "Tomomi Kato", "Issei Kobayashi", "Masao Yuda"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004905.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_a_missing_gene_in_the_P_berghei_genome_/1427617", "title"=>"Identification of a missing gene in the <i>P</i>. <i>berghei</i> genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-27 02:58:07"}

PMC Usage Stats | Further Information

  • {"unique-ip"=>"24", "full-text"=>"25", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2015", "month"=>"6"}
  • {"unique-ip"=>"30", "full-text"=>"31", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
  • {"unique-ip"=>"17", "full-text"=>"14", "pdf"=>"10", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"34", "full-text"=>"32", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"37", "full-text"=>"32", "pdf"=>"26", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"10", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"24", "full-text"=>"16", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"27", "full-text"=>"21", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"12", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"23", "full-text"=>"18", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"15", "full-text"=>"13", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"22", "full-text"=>"17", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"16", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
  • {"unique-ip"=>"27", "full-text"=>"29", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"4"}
  • {"unique-ip"=>"22", "full-text"=>"21", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"23", "full-text"=>"21", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
  • {"unique-ip"=>"24", "full-text"=>"20", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"15", "full-text"=>"11", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"11", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"12", "full-text"=>"10", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"9", "full-text"=>"11", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"19", "full-text"=>"21", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"16", "full-text"=>"23", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"11", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"15", "full-text"=>"14", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"12", "full-text"=>"17", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"18", "full-text"=>"25", "pdf"=>"10", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"17", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"11", "full-text"=>"13", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"10", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"15", "full-text"=>"14", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"15", "full-text"=>"14", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"21", "full-text"=>"23", "pdf"=>"11", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"13", "full-text"=>"13", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"14", "full-text"=>"10", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"14", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"12", "full-text"=>"8", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"10", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"10", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"10", "full-text"=>"44", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
Loading … Spinner
There are currently no alerts