Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation
Publication Date
December 29, 2015
Journal
PLOS Genetics
Authors
Santiago Naranjo, Justin D. Smith, Carlo G. Artieri, Mian Zhang, et al
Volume
11
Issue
12
Pages
e1005751
DOI
https://dx.plos.org/10.1371/journal.pgen.1005751
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1005751
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26713447
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694769
Europe PMC
http://europepmc.org/abstract/MED/26713447
Scopus
84953312182
Mendeley
http://www.mendeley.com/research/dissecting-genetic-basis-complex-cisregulatory-adaptation
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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/2618381"], "description"=>"<p><b>A.</b> Citrinin has largely similar effects on <i>Sc</i> alleles and <i>Sp</i> alleles in the <i>Sc</i>/<i>Sp</i> hybrid; i.e. ASE is similar with or without citrinin. <b>B.</b> Candidate genes were identified based on having strong <i>Sp</i>-biased ASE (in YPD; FDR < 0.05) [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005751#pgen.1005751.ref016\" target=\"_blank\">16</a>], and strong up-regulation in response to citrinin (of both <i>Sc</i> and <i>Sp</i> alleles; the smaller of these two in our RNA-seq data is plotted; binomial <i>p</i> < 10<sup>−5</sup> for each biological replicate of each allele).</p>", "links"=>[], "tags"=>["resistance", "basis", "polygenic adaptations", "citrinin", "yeast Saccharomyces paradoxus", "gene"], "article_id"=>1631376, "categories"=>["Biological Sciences"], "users"=>["Santiago Naranjo", "Justin D. Smith", "Carlo G. Artieri", "Mian Zhang", "Yiqi Zhou", "Michael E. Palmer", "Hunter B. Fraser"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005751.g003", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RNA_seq_reveals_candidate_genes_/1631376", "title"=>"RNA-seq reveals candidate genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:55:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2618383"], "description"=>"<p><b>A.</b> The five candidate genes were deleted from <i>Sp</i>, and the effect on resistance to 300 ppm citrinin was measured. Four deletions increased sensitivity (t-test <i>p</i> < 0.005 for each), and were studied further. Error bars show 1 S.E. <b>B.</b> The effects of three different dCas9 fusion proteins targeted to four candidate genes were measured by qPCR. <b>C.</b> Illustration of our strategy to over-express four genes via dCas9 fusion protein. <b>D.</b> We used direct competition for 40 generations to measure the relative fitness of the four-gene over-expression strain (with a Gal4-dCas9-VP64 dual fusion) vs. a control strain containing the same plasmid, but lacking any gRNAs. Conditions were YPD, and YPD + 300 ppm citrinin. Error bars show 1 S.E.</p>", "links"=>[], "tags"=>["resistance", "basis", "polygenic adaptations", "citrinin", "yeast Saccharomyces paradoxus", "gene"], "article_id"=>1631378, "categories"=>["Biological Sciences"], "users"=>["Santiago Naranjo", "Justin D. Smith", "Carlo G. Artieri", "Mian Zhang", "Yiqi Zhou", "Michael E. Palmer", "Hunter B. Fraser"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005751.g004", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effects_of_candidate_gene_deletion_and_over_expression_/1631378", "title"=>"Effects of candidate gene deletion and over-expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:55:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2618384"], "description"=>"<p><b>A.</b> Illustration of our promoter replacement strategy. Green promoters on the left are from <i>Sc</i>, blue promoters on the right are from <i>Sp</i>. <b>B.</b> RNA-seq in the <i>Sc</i>/<i>Sp</i> hybrid, which measures the overall <i>cis-</i>regulatory divergence between these strains, is in approximate agreement with the effect of the promoter replacements, measured by qPCR (<i>r</i> = 0.92). Error bars show 1 S.E. <b>C.</b> After competitive growth for 40 generations, promoter replacement strains for 3/4 candidate genes show a similar pattern of fitness advantage in the presence of 300 ppm citrinin, and disadvantage in its absence. Error bars show 1 S.E.</p>", "links"=>[], "tags"=>["resistance", "basis", "polygenic adaptations", "citrinin", "yeast Saccharomyces paradoxus", "gene"], "article_id"=>1631379, "categories"=>["Biological Sciences"], "users"=>["Santiago Naranjo", "Justin D. Smith", "Carlo G. Artieri", "Mian Zhang", "Yiqi Zhou", "Michael E. Palmer", "Hunter B. Fraser"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005751.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Promoter_replacement_reveals_contributions_of_individual_regulatory_regions_/1631379", "title"=>"Promoter replacement reveals contributions of individual regulatory regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:55:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/2618385", "https://ndownloader.figshare.com/files/2618386", "https://ndownloader.figshare.com/files/2618387", "https://ndownloader.figshare.com/files/2618388"], "description"=>"<div><p>Although single genes underlying several evolutionary adaptations have been identified, the genetic basis of complex, polygenic adaptations has been far more challenging to pinpoint. Here we report that the budding yeast <i>Saccharomyces paradoxus</i> has recently evolved resistance to citrinin, a naturally occurring mycotoxin. Applying a genome-wide test for selection on <i>cis</i>-regulation, we identified five genes involved in the citrinin response that are constitutively up-regulated in <i>S</i>. <i>paradoxus</i>. Four of these genes are necessary for resistance, and are also sufficient to increase the resistance of a sensitive strain when over-expressed. Moreover, <i>cis</i>-regulatory divergence in the promoters of these genes contributes to resistance, while exacting a cost in the absence of citrinin. Our results demonstrate how the subtle effects of individual regulatory elements can be combined, via natural selection, into a complex adaptation. Our approach can be applied to dissect the genetic basis of polygenic adaptations in a wide range of species.</p></div>", "links"=>[], "tags"=>["resistance", "basis", "polygenic adaptations", "citrinin", "yeast Saccharomyces paradoxus", "gene"], "article_id"=>1631380, "categories"=>["Biological Sciences"], "users"=>["Santiago Naranjo", "Justin D. Smith", "Carlo G. Artieri", "Mian Zhang", "Yiqi Zhou", "Michael E. Palmer", "Hunter B. Fraser"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005751.s001", "https://dx.doi.org/10.1371/journal.pgen.1005751.s002", "https://dx.doi.org/10.1371/journal.pgen.1005751.s003", "https://dx.doi.org/10.1371/journal.pgen.1005751.s004"], "stats"=>{"downloads"=>5, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Dissecting_the_Genetic_Basis_of_a_Complex_cis_Regulatory_Adaptation/1631380", "title"=>"Dissecting the Genetic Basis of a Complex <i>cis</i>-Regulatory Adaptation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-01-05 14:55:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2618378"], "description"=>"<p>For a description of the test and its results, see the main text and Methods. Note that only two citrinin-induced genes are shown, but four were present in the top 1% of <i>Sp</i>-biased genes, and ten in the top 25%.</p>", "links"=>[], "tags"=>["resistance", "basis", "polygenic adaptations", "citrinin", "yeast Saccharomyces paradoxus", "gene"], "article_id"=>1631373, "categories"=>["Biological Sciences"], "users"=>["Santiago Naranjo", "Justin D. Smith", "Carlo G. Artieri", "Mian Zhang", "Yiqi Zhou", "Michael E. Palmer", "Hunter B. Fraser"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005751.g001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_sign_test_for_selection_on_cis_regulation_/1631373", "title"=>"Results of the sign test for selection on <i>cis-</i>regulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:55:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/2618379"], "description"=>"<p><b>A.</b><i>Sc</i> growth at different concentrations of citrinin. Three replicates are shown for each condition. <b>B.</b><i>Sp</i> growth at different concentrations of citrinin. Three replicates are shown for each condition. <b>C.</b> Two metrics of resistance, maximum growth rate and maximum cell density, are shown for 25 <i>S</i>. <i>paradoxus</i> strains and <i>Sc</i>. Results are plotted as log-ratios relative to <i>Sc</i>. <b>D.</b> Citrinin resistance treated as a binary trait and plotted on a phylogenetic tree [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005751#pgen.1005751.ref044\" target=\"_blank\">44</a>]. The most parsimonious evolutionary scenario is shown in red text. Branch lengths are not to scale.</p>", "links"=>[], "tags"=>["resistance", "basis", "polygenic adaptations", "citrinin", "yeast Saccharomyces paradoxus", "gene"], "article_id"=>1631374, "categories"=>["Biological Sciences"], "users"=>["Santiago Naranjo", "Justin D. Smith", "Carlo G. Artieri", "Mian Zhang", "Yiqi Zhou", "Michael E. Palmer", "Hunter B. Fraser"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005751.g002", "stats"=>{"downloads"=>4, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sp_recently_evolved_resistance_to_citrinin_/1631374", "title"=>"<i>Sp</i> recently evolved resistance to citrinin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:55:09"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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