Rif1 Regulates Initiation Timing of Late Replication Origins throughout the S. cerevisiae Genome
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{"title"=>"Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome", "type"=>"journal", "authors"=>[{"first_name"=>"Jared M.", "last_name"=>"Peace", "scopus_author_id"=>"54912482200"}, {"first_name"=>"Anna", "last_name"=>"Ter-Zakarian", "scopus_author_id"=>"56204188900"}, {"first_name"=>"Oscar M.", "last_name"=>"Aparicio", "scopus_author_id"=>"6602858066"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24879017", "sgr"=>"84902350415", "doi"=>"10.1371/journal.pone.0098501", "scopus"=>"2-s2.0-84902350415", "pui"=>"373302235", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"2b6ef162-96eb-38cf-bc5d-2a428077e23a", "abstract"=>"Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. Rif1 has recently been identified as a genome-wide regulator of replication timing in fission yeast and in mammalian cells. However, previous studies in budding yeast have suggested that Rif1's role in controlling replication timing may be limited to subtelomeric domains and derives from its established role in telomere length regulation. We have analyzed replication timing by analyzing BrdU incorporation genome-wide, and report that Rif1 regulates the timing of late/dormant replication origins throughout the S. cerevisiae genome. Analysis of pfa4Δ cells, which are defective in palmitoylation and membrane association of Rif1, suggests that replication timing regulation by Rif1 is independent of its role in localizing telomeres to the nuclear periphery. Intra-S checkpoint signaling is intact in rif1Δ cells, and checkpoint-defective mec1Δ cells do not comparably deregulate replication timing, together indicating that Rif1 regulates replication timing through a mechanism independent of this checkpoint. Our results indicate that the Rif1 mechanism regulates origin timing irrespective of proximity to a chromosome end, and suggest instead that telomere sequences merely provide abundant binding sites for proteins that recruit Rif1. Still, the abundance of Rif1 binding in telomeric domains may facilitate Rif1-mediated repression of non-telomeric origins that are more distal from centromeres.", "link"=>"http://www.mendeley.com/research/rif1-regulates-initiation-timing-late-replication-origins-throughout-s-cerevisiae-genome", "reader_count"=>60, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>14, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>2, "Student > Master"=>8, "Student > Bachelor"=>11, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>14, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>2, "Student > Master"=>8, "Student > Bachelor"=>11, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>16, "Agricultural and Biological Sciences"=>36, "Chemistry"=>1, "Psychology"=>1, "Earth and Planetary Sciences"=>1, "Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"France"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1514821"], "description"=>"<p>Plots show BrdU incorporation in HU-arrested cells. Plot colors are keyed above. Boxed origins are labeled and discussed in the text.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA replication", "Nucleic acids", "cell biology", "Chromosome biology", "chromosomes", "Chromosome structure and function", "centromeres", "telomeres", "chromatin", "Molecular cell biology", "genetics", "genomics", "organisms", "fungi", "yeast", "saccharomyces", "Saccharomyces cerevisiae", "Model organisms", "Yeast and fungal models", "s-phase"], "article_id"=>1040816, "categories"=>["Biological Sciences"], "users"=>["Jared M. Peace", "Anna Ter-Zakarian", "Oscar M. Aparicio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098501.g001", "stats"=>{"downloads"=>4, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_early_S_phase_by_BrdU_chip_/1040816", "title"=>"Analysis of early S-phase by BrdU-chip.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-30 03:33:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1514822"], "description"=>"<p>Plot colors are keyed above. (<b>A, B</b>) Plots show average BrdU incorporation from duplicate experiments. Boxed origins and termination sites (TER) are labeled and discussed in the text. (<b>C, D</b>) Plots show average BrdU incorporation signals centered on origins in each T<sub>Rep</sub> quartile.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA replication", "Nucleic acids", "cell biology", "Chromosome biology", "chromosomes", "Chromosome structure and function", "centromeres", "telomeres", "chromatin", "Molecular cell biology", "genetics", "genomics", "organisms", "fungi", "yeast", "saccharomyces", "Saccharomyces cerevisiae", "Model organisms", "Yeast and fungal models", "replication"], "article_id"=>1040817, "categories"=>["Biological Sciences"], "users"=>["Jared M. Peace", "Anna Ter-Zakarian", "Oscar M. Aparicio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098501.g002", "stats"=>{"downloads"=>0, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_analysis_of_replication_by_BrdU_IP_chip_/1040817", "title"=>"Temporal analysis of replication by BrdU-IP-chip.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-30 03:33:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1514823"], "description"=>"<p>(<b>A</b>) Immunoblot analysis of Rad53 phosphorylation in cells released into HU. (<b>B</b>) DNA content analysis of cells released into MMS.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA replication", "Nucleic acids", "cell biology", "Chromosome biology", "chromosomes", "Chromosome structure and function", "centromeres", "telomeres", "chromatin", "Molecular cell biology", "genetics", "genomics", "organisms", "fungi", "yeast", "saccharomyces", "Saccharomyces cerevisiae", "Model organisms", "Yeast and fungal models", "intra-s", "checkpoint"], "article_id"=>1040818, "categories"=>["Biological Sciences"], "users"=>["Jared M. Peace", "Anna Ter-Zakarian", "Oscar M. Aparicio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098501.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_intra_S_checkpoint_response_/1040818", "title"=>"Analysis of intra-S checkpoint response.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-30 03:33:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1514824"], "description"=>"<p>Plot colors are keyed above. (<b>A</b>) Plots show average BrdU incorporation from duplicate experiments. Origin classes are color-coded below each plot. (<b>B</b>) Plots show average BrdU incorporation signals centered on origins in each T<sub>Rep</sub> quartile. (<b>C</b>) Plots show average BrdU incorporation signals centered on origins in each class as described in the text. (<b>D</b>) Origins are plotted along the x-axis according to T<sub>Rep</sub> rank and color-coded according to class and genomic location.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA replication", "Nucleic acids", "cell biology", "Chromosome biology", "chromosomes", "Chromosome structure and function", "centromeres", "telomeres", "chromatin", "Molecular cell biology", "genetics", "genomics", "organisms", "fungi", "yeast", "saccharomyces", "Saccharomyces cerevisiae", "Model organisms", "Yeast and fungal models", "s-phase"], "article_id"=>1040819, "categories"=>["Biological Sciences"], "users"=>["Jared M. Peace", "Anna Ter-Zakarian", "Oscar M. Aparicio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098501.g004", "stats"=>{"downloads"=>1, "page_views"=>100, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_early_S_phase_by_BrdU_IP_Seq_/1040819", "title"=>"Analysis of early S-phase by BrdU-IP-Seq.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-30 03:33:36"}
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Relative Metric

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