Genome-Wide Mapping Indicates That p73 and p63 Co-Occupy Target Sites and Have Similar DNA-Binding Profiles In Vivo
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{"title"=>"Genome-wide mapping indicates that p73 and p63 Co-occupy target sites and have similar DNA-binding profiles in vivo", "type"=>"journal", "authors"=>[{"first_name"=>"Annie", "last_name"=>"Yang", "scopus_author_id"=>"7203071361"}, {"first_name"=>"Zhou", "last_name"=>"Zhu", "scopus_author_id"=>"36479724700"}, {"first_name"=>"Arminja", "last_name"=>"Kettenbach", "scopus_author_id"=>"23019182500"}, {"first_name"=>"Philipp", "last_name"=>"Kapranov", "scopus_author_id"=>"6603162390"}, {"first_name"=>"Frank", "last_name"=>"McKeon", "scopus_author_id"=>"56752568100"}, {"first_name"=>"Thomas R.", "last_name"=>"Gingeras", "scopus_author_id"=>"7003527869"}, {"first_name"=>"Kevin", "last_name"=>"Struhl", "scopus_author_id"=>"7102602655"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203", "sgr"=>"77955351317", "doi"=>"10.1371/journal.pone.0011572", "scopus"=>"2-s2.0-77955351317", "pui"=>"359318702", "pmid"=>"20644729"}, "id"=>"5712ca7a-97b8-3dce-b842-0b6e971e64f4", "abstract"=>"BACKGROUND: The p53 homologs, p63 and p73, share approximately 85% amino acid identity in their DNA-binding domains, but they have distinct biological functions.\\n\\nPRINCIPAL FINDINGS: Using chromatin immunoprecipitation and high-resolution tiling arrays covering the human genome, we identify p73 DNA binding sites on a genome-wide level in ME180 human cervical carcinoma cells. Strikingly, the p73 binding profile is indistinguishable from the previously described binding profile for p63 in the same cells. Moreover, the p73:p63 binding ratio is similar at all genomic loci tested, suggesting that there are few, if any, targets that are specific for one of these factors. As assayed by sequential chromatin immunoprecipitation, p63 and p73 co-occupy DNA target sites in vivo, suggesting that p63 and p73 bind primarily as heterotetrameric complexes in ME180 cells.\\n\\nCONCLUSIONS: The observation that p63 and p73 associate with the same genomic targets suggest that their distinct biological functions are due to cell-type specific expression and/or protein domains that involve functions other than DNA binding.", "link"=>"http://www.mendeley.com/research/genomewide-mapping-indicates-p73-p63-cooccupy-target-sites-similar-dnabinding-profiles-vivo", "reader_count"=>24, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>17, "Medicine and Dentistry"=>3, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Turkey"=>1, "United States"=>3, "Russia"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/842126"], "description"=>"<p>Sequential chromatin immunoprecipitation (SeqChIP) samples were analyzed by quantitative PCR (qPCR) for p63 and p73 enrichment at various targets. Shown is the average occupancy value from 3 biological replicates. (A) p63 immunoprecipitation (1<sup>st</sup> IP) followed by p73 immunoprecipitation (2<sup>nd</sup> IP). (B) p73 immunoprecipitation (1<sup>st</sup> IP) followed by p63 immunoprecipitation (2<sup>nd</sup> IP). The fold-increase (2<sup>nd</sup> IP over 1<sup>st</sup> IP) in enrichment after sequential ChIP is indicated.</p>", "links"=>[], "tags"=>["p73", "co-occupancy"], "article_id"=>512583, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Annie Yang", "Zhou Zhu", "Arminja Kettenbach", "Philipp Kapranov", "Frank McKeon", "Thomas R. Gingeras", "Kevin Struhl"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011572.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_p63_and_p73_co_occupancy_in_vivo_/512583", "title"=>"p63 and p73 co-occupancy <i>in vivo</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-14 00:43:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/842036"], "description"=>"<p>Shown is the average occupancy value from 3 biological replicates. The ratio of p63 to p73 occupancy at each target site is indicated.</p>", "links"=>[], "tags"=>["p63", "p73"], "article_id"=>512491, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Annie Yang", "Zhou Zhu", "Arminja Kettenbach", "Philipp Kapranov", "Frank McKeon", "Thomas R. Gingeras", "Kevin Struhl"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011572.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparable_ratio_of_p63_and_p73_association_with_target_sites_/512491", "title"=>"Comparable ratio of p63 and p73 association with target sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-14 00:41:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/841870"], "description"=>"<p>(A) Overlap of p63 and p73 binding sites at three different significance thresholds. p63 binding sites were identified in our previous work <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011572#pone.0011572-Yang4\" target=\"_blank\">[24]</a>, and percentages of overlap are expressed with respect to p73 sites. (B) Correlation between p63 and p73 binding enrichment scores, which were defined as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011572#s2\" target=\"_blank\">Methods</a>. p63 scores are plotted as a moving average (window size = 50).</p>", "links"=>[], "tags"=>["p73", "dna-binding", "profiles", "me180"], "article_id"=>512325, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Annie Yang", "Zhou Zhu", "Arminja Kettenbach", "Philipp Kapranov", "Frank McKeon", "Thomas R. Gingeras", "Kevin Struhl"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011572.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_p63_and_p73_have_very_similar_DNA_binding_profiles_in_ME180_cells_/512325", "title"=>"p63 and p73 have very similar DNA-binding profiles in ME180 cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-14 00:38:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/418598", "https://ndownloader.figshare.com/files/418670", "https://ndownloader.figshare.com/files/418715"], "description"=>"<div><h3>Background</h3><p>The p53 homologs, p63 and p73, share ∼85% amino acid identity in their DNA-binding domains, but they have distinct biological functions.</p><h3>Principal Findings</h3><p>Using chromatin immunoprecipitation and high-resolution tiling arrays covering the human genome, we identify p73 DNA binding sites on a genome-wide level in ME180 human cervical carcinoma cells. Strikingly, the p73 binding profile is indistinguishable from the previously described binding profile for p63 in the same cells. Moreover, the p73∶p63 binding ratio is similar at all genomic loci tested, suggesting that there are few, if any, targets that are specific for one of these factors. As assayed by sequential chromatin immunoprecipitation, p63 and p73 co-occupy DNA target sites <em>in vivo</em>, suggesting that p63 and p73 bind primarily as heterotetrameric complexes in ME180 cells.</p><h3>Conclusions</h3><p>The observation that p63 and p73 associate with the same genomic targets suggest that their distinct biological functions are due to cell-type specific expression and/or protein domains that involve functions other than DNA binding.</p></div>", "links"=>[], "tags"=>["genome-wide", "indicates", "p73", "p63", "co-occupy", "sites", "dna-binding", "profiles"], "article_id"=>142660, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Annie Yang", "Zhou Zhu", "Arminja Kettenbach", "Philipp Kapranov", "Frank McKeon", "Thomas R. Gingeras", "Kevin Struhl"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0011572.s001", "https://dx.doi.org/10.1371/journal.pone.0011572.s002", "https://dx.doi.org/10.1371/journal.pone.0011572.s003"], "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Mapping_Indicates_That_p73_and_p63_Co_Occupy_Target_Sites_and_Have_Similar_DNA_Binding_Profiles_In_Vivo_/142660", "title"=>"Genome-Wide Mapping Indicates That p73 and p63 Co-Occupy Target Sites and Have Similar DNA-Binding Profiles <em>In Vivo</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-07-14 00:44:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/841711"], "description"=>"<p>(A) Evolutionary conservation is defined as the total percent identities of p73-bound sequences and 1000 groups of randomly selected comparable genomic sequences across multiple species. Error bars correspond to standard deviation from 1000 randomly sampled groups. (B) The DNA sequence motif for p73 derived <i>de novo</i> from the genomic binding sites is compared to the motif for p63 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011572#pone.0011572-Yang4\" target=\"_blank\">[24]</a> and p53. The p73 motif is essentially identical to the p63 response (CompareACE score = 0.95) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011572#pone.0011572-Hughes1\" target=\"_blank\">[34]</a>.</p>", "links"=>[], "tags"=>["dna", "motif", "p73-bound", "sites", "me180"], "article_id"=>512161, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Annie Yang", "Zhou Zhu", "Arminja Kettenbach", "Philipp Kapranov", "Frank McKeon", "Thomas R. Gingeras", "Kevin Struhl"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011572.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_conservation_and_DNA_sequence_motif_of_p73_bound_sites_in_ME180_cells_/512161", "title"=>"Evolutionary conservation and DNA sequence motif of p73-bound sites in ME180 cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-14 00:36:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/842250"], "description"=>"<p>Eluates were probed with anti-p73 (top gel) or anti-p63 (bottom gel) antibodies. lane 1: anti-p63 1st IP; lane 2: anti-p73 2nd IP; lane 3: anti-p73 1st IP; lane 4: anti-p63 2nd IP. Mw, molecular weight; kD, kiloDaltons, IgG, immunoglobulin.</p>", "links"=>[], "tags"=>["blot", "sequential", "chromatin", "immunoprecipiations", "p63"], "article_id"=>512703, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Annie Yang", "Zhou Zhu", "Arminja Kettenbach", "Philipp Kapranov", "Frank McKeon", "Thomas R. Gingeras", "Kevin Struhl"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011572.g005", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Western_blot_WB_analysis_of_sequential_chromatin_immunoprecipiations_for_p63_and_p73_/512703", "title"=>"Western blot (WB) analysis of sequential chromatin immunoprecipiations for p63 and p73.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-07-14 00:45:03"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"12"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"1"}
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Relative Metric

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