A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome
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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/422592", "https://ndownloader.figshare.com/files/422607", "https://ndownloader.figshare.com/files/422620", "https://ndownloader.figshare.com/files/422632", "https://ndownloader.figshare.com/files/422666", "https://ndownloader.figshare.com/files/422685", "https://ndownloader.figshare.com/files/422703", "https://ndownloader.figshare.com/files/422718", "https://ndownloader.figshare.com/files/422738", "https://ndownloader.figshare.com/files/422753", "https://ndownloader.figshare.com/files/422779", "https://ndownloader.figshare.com/files/422798", "https://ndownloader.figshare.com/files/422814"], "description"=>"<div><p>Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study the evolution of replication origins. However, to date, the <em>Saccharomyces cerevisiae</em> replication origin map is the only genome map available. Using an iterative approach that combines computational prediction and functional validation, we have generated a high-resolution genome-wide map of DNA replication origins in <em>Kluyveromyces lactis</em>. Unlike other yeasts or metazoans, <em>K. lactis</em> autonomously replicating sequences (<em>Kl</em>ARSs) contain a 50 bp consensus motif suggestive of a dimeric structure. This motif is necessary and largely sufficient for initiation and was used to dependably identify 145 of the up to 156 non-repetitive intergenic ARSs projected for the <em>K. lactis</em> genome. Though similar in genome sizes, <em>K. lactis</em> has half as many ARSs as its distant relative <em>S. cerevisiae</em>. Comparative genomic analysis shows that ARSs in <em>K. lactis</em> and <em>S. cerevisiae</em> preferentially localize to non-syntenic intergenic regions, linking ARSs with loci of accelerated evolutionary change.</p></div>", "links"=>[], "tags"=>["genome-wide", "autonomously", "replicating", "sequences", "naive", "genome"], "article_id"=>143456, "categories"=>["Genetics"], "users"=>["Ivan Liachko", "Anand Bhaskar", "Chanmi Lee", "Shau Chee Claire Chung", "Bik-Kwoon Tye", "Uri Keich"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000946.s001", "https://dx.doi.org/10.1371/journal.pgen.1000946.s002", "https://dx.doi.org/10.1371/journal.pgen.1000946.s003", "https://dx.doi.org/10.1371/journal.pgen.1000946.s004", "https://dx.doi.org/10.1371/journal.pgen.1000946.s005", "https://dx.doi.org/10.1371/journal.pgen.1000946.s006", "https://dx.doi.org/10.1371/journal.pgen.1000946.s007", "https://dx.doi.org/10.1371/journal.pgen.1000946.s008", "https://dx.doi.org/10.1371/journal.pgen.1000946.s009", "https://dx.doi.org/10.1371/journal.pgen.1000946.s010", "https://dx.doi.org/10.1371/journal.pgen.1000946.s011", "https://dx.doi.org/10.1371/journal.pgen.1000946.s012", "https://dx.doi.org/10.1371/journal.pgen.1000946.s013"], "stats"=>{"downloads"=>13, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Comprehensive_Genome_Wide_Map_of_Autonomously_Replicating_Sequences_in_a_Naive_Genome/143456", "title"=>"A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-05-13 00:57:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/849083"], "description"=>"<p>(A) Schematic of the ARS screen in <i>K. lactis</i>. (B) Schematic for the iterative predict-and-verify approach for identifying genomic ARSs. (C) Logos of <i>Kl</i>ACS <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000946#pgen.1000946-Crooks1\" target=\"_blank\">[66]</a>. Top panel, <i>Kl</i>ACS based on the initial 69 <i>Kl</i>ARSs. Bottom panel, <i>Kl</i>ACS based on 148 verified <i>Kl</i>ARSs. Arrows indicate an inverted repeat motif centered about an axis of symmetry marked by a vertical line. (D) An extended 50 bp motif of the <i>S. cerevisiae</i> ACS motif is shown in comparison with the <i>Kl</i>ACS.</p>", "links"=>[], "tags"=>["characterization"], "article_id"=>519533, "categories"=>["Genetics"], "users"=>["Ivan Liachko", "Anand Bhaskar", "Chanmi Lee", "Shau Chee Claire Chung", "Bik-Kwoon Tye", "Uri Keich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000946.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Isolation_and_characterization_of_K_lactis_ARSs_/519533", "title"=>"Isolation and characterization of <i>K. lactis</i> ARSs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-13 02:38:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/849423"], "description"=>"<p>10 randomly chosen <i>Kl</i>ARSs and three non-ARS sequences were analyzed. The name of the ARS tested in its genomic context is indicated below each picture. Red arrows indicate “bubble arcs” caused by replication initiation events at probed loci. All experiments were performed on asynchronous log-phase cultures.</p>", "links"=>[], "tags"=>["replication", "initiation", "shown", "2d", "gel"], "article_id"=>519870, "categories"=>["Genetics"], "users"=>["Ivan Liachko", "Anand Bhaskar", "Chanmi Lee", "Shau Chee Claire Chung", "Bik-Kwoon Tye", "Uri Keich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000946.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_replication_initiation_shown_by_2D_gel_electrophoresis_/519870", "title"=>"Genomic replication initiation shown by 2D gel electrophoresis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-13 02:44:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/849501"], "description"=>"<p>(A) Overlapping ACSs of KARS12 (<i>Kl</i>ARS503) as predicted previously <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000946#pgen.1000946-Irene1\" target=\"_blank\">[29]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000946#pgen.1000946-Irene2\" target=\"_blank\">[30]</a> (colored in green) and in this study (colored in blue). Substitution mutations are shown in lower case font and deletions in dashes. Mutations that disrupt ARS function are highlighted in red, and mutations that do not affect ARS function are highlighted in black. The logo of 50bp ACS is superimposed for reference. (+) indicates ARS function and (−) indicates no ARS function. (B) Complete overlapping ACSs (colored in blue) of KARS101 identified by linker substitution analysis <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000946#pgen.1000946-Fabiani1\" target=\"_blank\">[28]</a> and by motif search in this study. Octanucleotide linker mutations that destroyed ARS function (−) are indicated by red bars and those that compromised ARS function (+/−) are indicated by grey bars. The logo of 50bp ACS is superimposed for reference.</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/bioinformatics", "genetics and genomics/chromosome biology", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics"], "article_id"=>519945, "categories"=>["Genetics"], "users"=>["Ivan Liachko", "Anand Bhaskar", "Chanmi Lee", "Shau Chee Claire Chung", "Bik-Kwoon Tye", "Uri Keich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000946.g006", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_KARS12_and_KARS101_two_previously_identified_Kl_ARSs_/519945", "title"=>"KARS12 and KARS101, two previously identified <i>Kl</i>ARSs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-13 02:45:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/849175"], "description"=>"<p>The 6 <i>K. lactis</i> chromosomes are shown in green with red blocks representing the <i>Kl</i>ARSs (<i>Kl</i>ARS size not to scale). The scale represents Megabases of genomic DNA.</p>", "links"=>[], "tags"=>["genomic", "locations"], "article_id"=>519629, "categories"=>["Genetics"], "users"=>["Ivan Liachko", "Anand Bhaskar", "Chanmi Lee", "Shau Chee Claire Chung", "Bik-Kwoon Tye", "Uri Keich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000946.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_representation_of_genomic_locations_of_Kl_ARSs_/519629", "title"=>"A representation of genomic locations of <i>Kl</i>ARSs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-13 02:40:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/849318"], "description"=>"<p>(A) Site-directed mutagenesis was used to replace trinucleotides in <i>Kl</i>ARS515. The mutant plasmids were tested for ARS activity. The mutated bases are underlined, and ARS function is indicated on the left and by the text color of the mutated nucleotides. The predicted <i>Kl</i>ACS motif is highlighted in blue. Mutants that did not affect function (+) are highlighted in black, while mutants affecting ARS function (+/− and −) are colored in red. Mutants that completely destroyed ARS function are indicated as (−), mutants that support the growth of minute colonies but contain dead cells on restreaking are indicated as (+/−) and mutants that had no effect are indicated as (+). Numbers on the right of the sequences are shown for reference. (B) Pictures of <i>K. lactis</i> transformed with mutant ARS plasmids on selective medium plates after 6 days of growth at 30°C. Plasmids with ARS activity comparable to the wild type plasmid (ARS+) are shown on the top row. Plasmids with weak ARS activity (ARS+/−) are shown in the middle row. Plasmids which show no visible ARS activity (ARS-) are on the bottom row. Numbers above the pictures correspond to mutant constructs from Figure 4A. Multiple clones of all plasmids were tested. Representative plasmids are shown. (C) ARS sequences of <i>Kl</i>ARS618, <i>Kl</i>ARS612 and <i>Kl</i>ARS524 were mutagenized to test the necessity of the predicted <i>Kl</i>ACS motif for ARS function. In all cases (6 total, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000946#pgen.1000946.s012\" target=\"_blank\">Table S1</a>) the predicted mutation destroyed <i>Kl</i>ARS function. Each of the full <i>Kl</i>ARS sequences is 451bp. (D) DNA flanking the <i>Kl</i>ACS motif was truncated and the resulting sequences were tested for ARS function. The number of shortened <i>Kl</i>ARSs that retained function is shown on the right and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000946#pgen.1000946.s012\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/bioinformatics", "genetics and genomics/chromosome biology", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics"], "article_id"=>519758, "categories"=>["Genetics"], "users"=>["Ivan Liachko", "Anand Bhaskar", "Chanmi Lee", "Shau Chee Claire Chung", "Bik-Kwoon Tye", "Uri Keich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000946.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kl_ACS_is_necessary_and_largely_sufficient_for_Kl_ARS_function_/519758", "title"=>"<i>Kl</i>ACS is necessary and largely sufficient for <i>Kl</i>ARS function.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-13 02:42:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/849234"], "description"=>"<p>ARSs from <i>S. cerevisiae</i> and <i>K. lactis</i> genomes are categorized with respect to flanking transcription. The headings display the transcription direction from the genes flanking the ARS.</p>", "links"=>[], "tags"=>["transcripts", "flanking"], "article_id"=>519681, "categories"=>["Genetics"], "users"=>["Ivan Liachko", "Anand Bhaskar", "Chanmi Lee", "Shau Chee Claire Chung", "Bik-Kwoon Tye", "Uri Keich"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000946.g003", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Orientation_of_transcripts_flanking_S_cerevisiae_and_K_lactis_ARSs_/519681", "title"=>"Orientation of transcripts flanking <i>S. cerevisiae</i> and <i>K. lactis</i> ARSs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-13 02:41:21"}

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