Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor
Publication Date
October 24, 2007
Journal
PLOS ONE
Authors
Caitlin M. Conboy, Christiana Spyrou, Natalie P. Thorne, Elizabeth J. Wade, et al
Volume
2
Issue
10
Pages
e1061
DOI
https://dx.plos.org/10.1371/journal.pone.0001061
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0001061
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/17957245
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2020443
Europe PMC
http://europepmc.org/abstract/MED/17957245
Web of Science
000207458500008
Scopus
42349088542
Mendeley
http://www.mendeley.com/research/cell-cycle-genes-evolutionarily-conserved-targets-e2f4-transcription-factor
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/464723", "https://ndownloader.figshare.com/files/464756", "https://ndownloader.figshare.com/files/464783", "https://ndownloader.figshare.com/files/464795", "https://ndownloader.figshare.com/files/464996", "https://ndownloader.figshare.com/files/465040", "https://ndownloader.figshare.com/files/465085", "https://ndownloader.figshare.com/files/465109"], "description"=>"<div><p>Maintaining quiescent cells in G0 phase is achieved in part through the multiprotein subunit complex known as DREAM, and in human cell lines the transcription factor E2F4 directs this complex to its cell cycle targets. We found that E2F4 binds a highly overlapping set of human genes among three diverse primary tissues and an asynchronous cell line, which suggests that tissue-specific binding partners and chromatin structure have minimal influence on E2F4 targeting. To investigate the conservation of these transcription factor binding events, we identified the mouse genes bound by E2f4 in seven primary mouse tissues and a cell line. E2f4 bound a set of mouse genes that was common among mouse tissues, but largely distinct from the genes bound in human. The evolutionarily conserved set of E2F4 bound genes is highly enriched for functionally relevant regulatory interactions important for maintaining cellular quiescence. In contrast, we found minimal mRNA expression perturbations in this core set of E2f4 bound genes in the liver, kidney, and testes of <em>E2f4</em> null mice. Thus, the regulatory mechanisms maintaining quiescence are robust even to complete loss of conserved transcription factor binding events.</p></div>", "links"=>[], "tags"=>["genes", "are", "evolutionarily", "conserved", "targets", "e2f4", "transcription"], "article_id"=>151594, "categories"=>["Genetics", "Biochemistry", "Biological Sciences", "Cancer", "Medicine"], "users"=>["Caitlin M. Conboy", "Christiana Spyrou", "Natalie P. Thorne", "Elizabeth J. Wade", "Nuno L. Barbosa-Morais", "Michael D. Wilson", "Arindam Bhattacharjee", "Richard A. Young", "Simon Tavaré", "Jacqueline A. Lees", "Duncan T. Odom"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0001061.s001", "https://dx.doi.org/10.1371/journal.pone.0001061.s002", "https://dx.doi.org/10.1371/journal.pone.0001061.s003", "https://dx.doi.org/10.1371/journal.pone.0001061.s004", "https://dx.doi.org/10.1371/journal.pone.0001061.s005", "https://dx.doi.org/10.1371/journal.pone.0001061.s006", "https://dx.doi.org/10.1371/journal.pone.0001061.s007", "https://dx.doi.org/10.1371/journal.pone.0001061.s008"], "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Cell_Cycle_Genes_Are_the_Evolutionarily_Conserved_Targets_of_the_E2F4_Transcription_Factor/151594", "title"=>"Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-10-24 00:26:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/943280"], "description"=>"<p>(A) Transcription factor binding was identified <i>in vivo</i> using chromatin immunoprecipitation combined with proximal promoter arrays in three human tissues, a human cell line, seven mouse tissues, and a mouse cell line. (B) Gene expression in the liver, kidney, and testes of littermate mice lacking one or two copies of E2f4 were compared in replicate, and genes specifically perturbed in the adult identified in all three tissues. (C) Analysis approaches identified the genes bound in common among all human and all mouse tissues, those shared between species, and whether any genes were both bound by E2f4 in mouse adult liver, kidney, or testes, and whose expression were altered by removal of E2f4.</p>", "links"=>[], "tags"=>["e2f4", "bound"], "article_id"=>613667, "categories"=>["Genetics", "Biochemistry", "Computational Biology", "Infectious Diseases", "Medicine"], "users"=>["Caitlin M. Conboy", "Christiana Spyrou", "Natalie P. Thorne", "Elizabeth J. Wade", "Nuno L. Barbosa-Morais", "Michael D. Wilson", "Arindam Bhattacharjee", "Richard A. Young", "Simon Tavaré", "Jacqueline A. Lees", "Duncan T. Odom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001061.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strategy_to_compare_E2F4_bound_and_E2F4_dependent_gene_expression_in_mouse_and_human_/613667", "title"=>"Strategy to compare E2F4 bound and E2F4 dependent gene expression in mouse and human.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-24 01:01:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/943533"], "description"=>"<p>(A) The complete list of genes that were differentially expressed when E2f4 was removed where the proximal promoter of these transcripts was present on the mouse promoter array. Genes were sorted by confidence in kidney, liver, and testes, sequentially, and the binding data then obtained separately. Most gene expression changes were tissue-specific, and very few of these genes showed in vivo E2f4 binding. (B) The complete list of genes bound by E2f4 in kidney, liver, and testes, clustered by transcription factor binding in each tissue sequentially. The transcripts of almost no genes bound in vivo were perturbed in the adult <i>E2f4</i> null mice.</p>", "links"=>[], "tags"=>["germline", "e2f4", "transcription", "binding", "testes", "poorly", "overlap", "genes", "bound", "mice", "containing"], "article_id"=>613916, "categories"=>["Genetics", "Biochemistry", "Computational Biology", "Infectious Diseases", "Medicine"], "users"=>["Caitlin M. Conboy", "Christiana Spyrou", "Natalie P. Thorne", "Elizabeth J. Wade", "Nuno L. Barbosa-Morais", "Michael D. Wilson", "Arindam Bhattacharjee", "Richard A. Young", "Simon Tavaré", "Jacqueline A. Lees", "Duncan T. Odom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001061.g003", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_changes_upon_germline_removal_of_E2f4_transcription_factor_binding_in_mouse_liver_kidney_and_testes_are_minimal_and_poorly_overlap_the_genes_bound_in_mice_containing_E2f4_/613916", "title"=>"Gene expression changes upon germline removal of E2f4 transcription factor binding in mouse liver, kidney, and testes are minimal, and poorly overlap the genes bound in mice containing E2f4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-24 01:05:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/943435"], "description"=>"<p>(A) Fraction of overlap of human genes bound by E2F4 in liver, pancreatic islets, pancreatic acinar, and HepG2 is shown as a grayscale shaded graph. Fractions and shading are calculated relative to the tissue with the fewest bound genes. The total number of binding targets for each tissue is shown in white boxes. (B) Similar plot for the overlap of mouse genes bound by E2f4 in liver, spleen, kidney, brain, testes, pancreatic islets, pancreatic acinar, and Min6. (C) Overlap between the mouse and human genes bound in common in all mouse and human tissues where homologs exist between the species. Consistent with previous results <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001061#pone.0001061-Odom1\" target=\"_blank\">[23]</a>, the overlap is approximately 20%. (D) The genes bound by E2F4 in both mouse and human are substantially enriched in genes accounting for E2F4 function.</p>", "links"=>[], "tags"=>["binding", "e2f4"], "article_id"=>613829, "categories"=>["Genetics", "Biochemistry", "Computational Biology", "Infectious Diseases", "Medicine"], "users"=>["Caitlin M. Conboy", "Christiana Spyrou", "Natalie P. Thorne", "Elizabeth J. Wade", "Nuno L. Barbosa-Morais", "Michael D. Wilson", "Arindam Bhattacharjee", "Richard A. Young", "Simon Tavaré", "Jacqueline A. Lees", "Duncan T. Odom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001061.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_binding_of_E2F4_in_mouse_and_human_tissues_/613829", "title"=>"Genome-wide binding of E2F4 in mouse and human tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-24 01:03:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/943615"], "description"=>"<p>Organized by GO categories, top hits by significance with p-values and binding ratios.</p>", "links"=>[], "tags"=>["categorization", "genes", "bound"], "article_id"=>614003, "categories"=>["Genetics", "Biochemistry", "Computational Biology", "Infectious Diseases", "Medicine"], "users"=>["Caitlin M. Conboy", "Christiana Spyrou", "Natalie P. Thorne", "Elizabeth J. Wade", "Nuno L. Barbosa-Morais", "Michael D. Wilson", "Arindam Bhattacharjee", "Richard A. Young", "Simon Tavaré", "Jacqueline A. Lees", "Duncan T. Odom"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001061.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_categorization_of_genes_bound_commonly_among_human_tissues_/614003", "title"=>"Functional categorization of genes bound commonly among human tissues.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-10-24 01:06:43"}

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Relative Metric

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