Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects
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{"title"=>"Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects", "type"=>"journal", "authors"=>[{"first_name"=>"Stephen Gregory", "last_name"=>"Addinall", "scopus_author_id"=>"6603545024"}, {"first_name"=>"Eva Maria", "last_name"=>"Holstein", "scopus_author_id"=>"37088485100"}, {"first_name"=>"Conor", "last_name"=>"Lawless", "scopus_author_id"=>"12545116100"}, {"first_name"=>"Min", "last_name"=>"Yu", "scopus_author_id"=>"49561978600"}, {"first_name"=>"Kaye", "last_name"=>"Chapman", "scopus_author_id"=>"16027898700"}, {"first_name"=>"A. Peter", "last_name"=>"Banks", "scopus_author_id"=>"38961104400"}, {"first_name"=>"Hien Ping", "last_name"=>"Ngo", "scopus_author_id"=>"7005488502"}, {"first_name"=>"Laura", "last_name"=>"Maringele", "scopus_author_id"=>"8086590100"}, {"first_name"=>"Morgan", "last_name"=>"Taschuk", "scopus_author_id"=>"8623907000"}, {"first_name"=>"Alexander", "last_name"=>"Young", "scopus_author_id"=>"56221264200"}, {"first_name"=>"Adam", "last_name"=>"Ciesiolka", "scopus_author_id"=>"36522594600"}, {"first_name"=>"Allyson Lurena", "last_name"=>"Lister", "scopus_author_id"=>"23489528800"}, {"first_name"=>"Anil", "last_name"=>"Wipat", "scopus_author_id"=>"6602761323"}, {"first_name"=>"Darren James", "last_name"=>"Wilkinson", "scopus_author_id"=>"7401870210"}, {"first_name"=>"David", "last_name"=>"Lydall", "scopus_author_id"=>"6604046439"}], "year"=>2011, "source"=>"PLoS Genetics", "identifiers"=>{"isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"21490951", "pui"=>"361703309", "issn"=>"15537390", "scopus"=>"2-s2.0-79955574694", "sgr"=>"79955574694", "doi"=>"10.1371/journal.pgen.1001362"}, "id"=>"8071d893-2568-376c-b7de-17b3aafd363d", "abstract"=>"To better understand telomere biology in budding yeast, we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation in the essential telomere capping gene CDC13 (cdc13-1) or containing a null mutation in the DNA damage response and telomere capping gene YKU70 (yku70Δ). We performed Quantitative Fitness Analysis (QFA) on thousands of yeast strains containing mutations affecting telomere-capping proteins in combination with a library of systematic gene deletion mutations. To perform QFA, we typically inoculate 384 separate cultures onto solid agar plates and monitor growth of each culture by photography over time. The data are fitted to a logistic population growth model; and growth parameters, such as maximum growth rate and maximum doubling potential, are deduced. QFA reveals that as many as 5% of systematic gene deletions, affecting numerous functional classes, strongly interact with telomere capping defects. We show that, while Cdc13 and Yku70 perform complementary roles in telomere capping, their genetic interaction profiles differ significantly. At least 19 different classes of functionally or physically related proteins can be identified as interacting with cdc13-1, yku70Δ, or both. Each specific genetic interaction informs the roles of individual gene products in telomere biology. One striking example is with genes of the nonsense-mediated RNA decay (NMD) pathway which, when disabled, suppress the conditional cdc13-1 mutation but enhance the null yku70Δ mutation. We show that the suppressing/enhancing role of the NMD pathway at uncapped telomeres is mediated through the levels of Stn1, an essential telomere capping protein, which interacts with Cdc13 and recruitment of telomerase to telomeres. We show that increased Stn1 levels affect growth of cells with telomere capping defects due to cdc13-1 and yku70Δ. QFA is a sensitive, high-throughput method that will also be useful to understand other aspects of microbial cell biology.", "link"=>"http://www.mendeley.com/research/quantitative-fitness-analysis-shows-nmd-proteins-other-protein-complexes-suppress-enhance-distinct-t", "reader_count"=>57, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>15, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>15, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>8, "Mathematics"=>1, "Agricultural and Biological Sciences"=>43, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Chemical Engineering"=>1, "Computer Science"=>1, "Environmental Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>43}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Mathematics"=>{"Mathematics"=>1}, "Environmental Science"=>{"Environmental Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>3, "United Kingdom"=>4, "Israel"=>1, "Germany"=>1, "India"=>2}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/785722"], "description"=>"<p>The number and percentage of gene deletions showing strong genetic interactions (|GIS|≥0.5) in each of the outer regions shown in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen-1001362-g003\" target=\"_blank\">Figure 3</a>.</p>", "links"=>[], "tags"=>["deletions", "regions", "shown"], "article_id"=>456076, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_and_proportion_of_deletions_in_each_of_the_nine_regions_shown_in_Figure_3_/456076", "title"=>"Number and proportion of deletions in each of the nine regions shown in Figure 3.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-07 01:41:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/784920"], "description"=>"<p>A) Time course images of eight independent <i>upf2</i>Δ <i>ura3</i>Δ, <i>yku70</i>Δ <i>ura3</i>Δ and <i>upf2</i>Δ <i>yku70</i>Δ strains at the indicated temperatures; B) Cell density of individual replicate cultures was determined after image-analysis. The logistic growth model is fitted to each culture density time-series. The same data are plotted on linear or logarithmic scales on left and right respectively. C) Average values for Maximum Doubling Rate, Maximum Doubling Potential and Fitness (MDR, MDP and F respectively; see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen.1001362.s014\" target=\"_blank\">Text S1</a>, experimental procedures), determined from the fitted curves. Data for <i>yku70</i>Δ <i>ura3</i>Δ is presented here to illustrate epistasis between <i>yku70</i>Δ and <i>upf3</i>Δ, however this is not how epistasis was calculated (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen-1001362-g002\" target=\"_blank\">Figure 2</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen.1001362.s014\" target=\"_blank\">Text S1</a>, experimental procedures).</p>", "links"=>[], "tags"=>["agar", "plates", "quantitative"], "article_id"=>455272, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cell_fitness_determination_from_growth_on_agar_plates_for_quantitative_fitness_analysis_QFA_/455272", "title"=>"Cell fitness determination from growth on agar plates for quantitative fitness analysis (QFA).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-07 01:27:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/785667"], "description"=>"<p>Genes that affect growth of <i>cdc13-1</i> mutants, <i>yku70</i>Δ mutants or both. Genes in ( ) brackets are known components of complexes not co-located. This is either because the deletion is missing from our collection or because the gene deletion is in a different position because, for example, deleting the gene affects the function of the adjacent gene also therefore causing a confounding phenotype. Genes in [ ] brackets are associated with the NMD pathway but have different phenotypes and are located in different positions on the plot.</p>", "links"=>[], "tags"=>["interacting", "telomere"], "article_id"=>456023, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.t003", "stats"=>{"downloads"=>5, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_interacting_with_the_telomere_cap_/456023", "title"=>"Genes interacting with the telomere cap.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-07 01:40:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/785622"], "description"=>"<p>We examined the effects of 4,120 gene deletions, ignoring deletions that were technically problematic (e.g. displayed linkage with query mutation, affected uracil, leucine or histidine biosynthesis). The table above shows percentages classified as significant suppressors (FDR corrected q-value <0.05, +ve GIS) or significant enhancers (FDR corrected q-value <0.05, -ve GIS) and with strong interactions (|GIS| ≥0.5).</p>", "links"=>[], "tags"=>["deletions", "suppressing", "enhancing", "query", "mutation", "defects", "qfa"], "article_id"=>455970, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.t001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_deletions_suppressing_or_enhancing_query_mutation_fitness_defects_in_specific_QFA_screens_/455970", "title"=>"Percentage of deletions suppressing or enhancing query mutation fitness defects in specific QFA screens.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-07 01:39:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/785047"], "description"=>"<p>The yeast genome knock out collection was crossed to the <i>yku70</i>Δ mutation, or as a control to the <i>ura3</i>Δ mutation. 8 replicate crosses were performed and for each, the fitness of all double mutant cultures measured as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen-1001362-g001\" target=\"_blank\">Figure 1</a>. Growth of <i>yku70</i>Δ <i>yfg</i>Δ (“<i>your favourite gene deletion</i>”) double mutants was measured at 37.5°C and <i>ura3</i>Δ <i>yfg</i>Δ strains at 37°C. Gene deletions that significantly enhance (green) or suppress (red) the <i>yku70</i>Δ defect, in comparison with the <i>ura3</i>Δ mutation are indicated. Those marked by open circles have p-values <0.05 and those filled circles have FDR corrected p-values (q-values) <0.05. The line of equal growth (dashed grey) and a population model of expected fitness (solid grey) are indicated. The average position of <i>his3</i>Δ strains are indicated by solid light-blue lines on each axis, as proxy for “wild-type” growth.</p>", "links"=>[], "tags"=>["strains"], "article_id"=>455407, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fitness_of_yku70_strains_at_high_temperature_/455407", "title"=>"Fitness of <i>yku70</i>Δ strains at high temperature.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-07 01:30:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/394803", "https://ndownloader.figshare.com/files/394813", "https://ndownloader.figshare.com/files/394829", "https://ndownloader.figshare.com/files/394859", "https://ndownloader.figshare.com/files/394882", "https://ndownloader.figshare.com/files/394888", "https://ndownloader.figshare.com/files/394898", "https://ndownloader.figshare.com/files/394910", "https://ndownloader.figshare.com/files/394920", "https://ndownloader.figshare.com/files/394933", "https://ndownloader.figshare.com/files/394951", "https://ndownloader.figshare.com/files/395002", "https://ndownloader.figshare.com/files/395033", "https://ndownloader.figshare.com/files/395043"], "description"=>"<div><p>To better understand telomere biology in budding yeast, we have performed systematic suppressor/enhancer analyses on yeast strains containing a point mutation in the essential telomere capping gene <em>CDC13</em> (<em>cdc13-1</em>) or containing a null mutation in the DNA damage response and telomere capping gene <em>YKU70</em> (<em>yku70</em>Δ). We performed Quantitative Fitness Analysis (QFA) on thousands of yeast strains containing mutations affecting telomere-capping proteins in combination with a library of systematic gene deletion mutations. To perform QFA, we typically inoculate 384 separate cultures onto solid agar plates and monitor growth of each culture by photography over time. The data are fitted to a logistic population growth model; and growth parameters, such as maximum growth rate and maximum doubling potential, are deduced. QFA reveals that as many as 5% of systematic gene deletions, affecting numerous functional classes, strongly interact with telomere capping defects. We show that, while Cdc13 and Yku70 perform complementary roles in telomere capping, their genetic interaction profiles differ significantly. At least 19 different classes of functionally or physically related proteins can be identified as interacting with <em>cdc13-1</em>, <em>yku70</em>Δ, or both. Each specific genetic interaction informs the roles of individual gene products in telomere biology. One striking example is with genes of the nonsense-mediated RNA decay (NMD) pathway which, when disabled, suppress the conditional <em>cdc13-1</em> mutation but enhance the null <em>yku70</em>Δ mutation. We show that the suppressing/enhancing role of the NMD pathway at uncapped telomeres is mediated through the levels of Stn1, an essential telomere capping protein, which interacts with Cdc13 and recruitment of telomerase to telomeres. We show that increased Stn1 levels affect growth of cells with telomere capping defects due to <em>cdc13-1</em> and <em>yku70</em>Δ. QFA is a sensitive, high-throughput method that will also be useful to understand other aspects of microbial cell biology.</p></div>", "links"=>[], "tags"=>["quantitative", "shows", "nmd", "proteins", "complexes", "suppress", "telomere", "defects"], "article_id"=>137981, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1001362.s001", "https://dx.doi.org/10.1371/journal.pgen.1001362.s002", "https://dx.doi.org/10.1371/journal.pgen.1001362.s003", "https://dx.doi.org/10.1371/journal.pgen.1001362.s004", "https://dx.doi.org/10.1371/journal.pgen.1001362.s005", "https://dx.doi.org/10.1371/journal.pgen.1001362.s006", "https://dx.doi.org/10.1371/journal.pgen.1001362.s007", "https://dx.doi.org/10.1371/journal.pgen.1001362.s008", "https://dx.doi.org/10.1371/journal.pgen.1001362.s009", "https://dx.doi.org/10.1371/journal.pgen.1001362.s010", "https://dx.doi.org/10.1371/journal.pgen.1001362.s011", "https://dx.doi.org/10.1371/journal.pgen.1001362.s012", "https://dx.doi.org/10.1371/journal.pgen.1001362.s013", "https://dx.doi.org/10.1371/journal.pgen.1001362.s014"], "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Quantitative_Fitness_Analysis_Shows_That_NMD_Proteins_and_Many_Other_Protein_Complexes_Suppress_or_Enhance_Distinct_Telomere_Cap_Defects/137981", "title"=>"Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-04-07 02:13:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/785450"], "description"=>"<p>A) Transcript levels of four telomere-binding factors measured in <i>upf2</i>Δ and <i>ebs1</i>Δ mutants. Four strains of each genotype were grown exponentially in liquid culture at 23°C. RNA was isolated and transcript levels were determined by SYBR Green RT-PCR. Each measurement was performed in triplicate and error bars indicate standard deviation from four independent measurements. RNA concentrations of the samples were normalized to the loading control <i>BUD6</i>. A single wild type sample was given the value of 1 and all other values were corrected relative to this. Strains measured are 640, 2824, 3001, 4763, 4764, 4765, 4766, 4780, 4781, 4782, 4783 and 4784; B) Western blot analysis of Stn1 protein levels using antibodies against Stn1-13Myc tagged strains. Strains shown are 5757, 5758, 5759, 5760, 5761, 5763, 5764, 5765 and 5766; C) Growth analysis of <i>yku70</i>Δ or <i>cdc13-1</i> mutants over-expressing <i>STN1</i> using the centromeric plasmid pVl1045. The empty vector Ycplac111 was used as a control. Strains 5046, 5047, 5051 and 5052 were spot tested on –LEU medium; D) <i>upf2</i>Δ and <i>ebs1</i>Δ mutants were combined with <i>yku70</i>Δ or <i>cdc13-1</i> mutations in the W303 genetic background and assessed for growth by spot test. Strains shown are 640 and 3001 (wild type), 2764 and 2824 (<i>ebs1</i>Δ), 2787 and 4309 (<i>yku70</i>Δ), 2889 and 2890 (<i>ebs1</i>Δ <i>yku70</i>Δ), 5007 and 5008 (<i>nmd2</i>Δ <i>yku70</i>Δ), 5251 and 5242 (<i>ebs1</i>Δ <i>nmd2</i>Δ <i>yku70</i>Δ), 1195 and 4557 (<i>cdc13-1</i>), 4576 and 4577 (<i>ebs1</i>Δ <i>cdc13-1</i>), 4624 and 4625 (<i>nmd2</i>Δ <i>cdc13-1</i>), 5238 and 5239 (<i>ebs1</i>Δ <i>nmd2</i>Δ <i>cdc13-1</i>); E) ChIP analysis of Est2-13Myc association to the VI-R telomere and the internal locus PDI1 on Chromosome III using primers previously described <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen.1001362-Bianchi1\" target=\"_blank\">[50]</a>. Duplicate cultures were grown and harvested in exponential phase. Individual ChIP samples were measured in triplicate and group means are shown with 95% confidence bars derived from a two-way ANOVA. Strains shown are 6977 (Est2-13Myc), 6978 (<i>nmd2</i>Δ Est2-13Myc), 6979 (<i>nmd2</i>Δ <i>yku70</i>Δ Est2-13Myc) and 6980 (<i>yku70</i>Δ Est2-13Myc).</p>", "links"=>[], "tags"=>["influences", "telomere", "capping", "telomerase"], "article_id"=>455800, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.g005", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_UPF2_influences_telomere_capping_through_STN1_and_telomerase_recruitment_/455800", "title"=>"<i>UPF2</i> influences telomere capping through <i>STN1</i> and telomerase recruitment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-07 01:36:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/785164"], "description"=>"<p>Genes that significantly interacted with <i>cdc13-1</i> or <i>yku70</i>Δ are shown, most genes did not interact and would be placed in the centre of the plot. Genes encoding components of selected protein complexes (or proteins which work closely together towards the same function) are indicated by colour-co-ordinated text and symbols. Genes that interact with both <i>cdc13-1</i> and <i>yku70</i>Δ are open white circles, those that interact with just one mutation are filled white circles. Different regions of the plot are indicated on the top right and borders between regions are intentionally blurred/overlapping as there are not precise cut-offs. An arbitrary GIS cutoff of +/−0.5 is indicated by the black dashed rectangle. Also see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen.1001362.s003\" target=\"_blank\">Figure S3</a> for further analysis of these data.</p>", "links"=>[], "tags"=>["computational biology/systems biology", "genetics and genomics/chromosome biology", "genetics and genomics/functional genomics"], "article_id"=>455522, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.g003", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_interaction_strength_GIS_comparison_between_cdc13_1_and_yku70_/455522", "title"=>"Genetic interaction strength (GIS) comparison between <i>cdc13-1</i> and <i>yku70</i>Δ.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-07 01:32:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/785317"], "description"=>"<p>A selection of genes identified by QFA were combined with either the <i>yku70</i>Δ or <i>cdc13-1</i> mutations in the W303 genetic background and assessed for growth by manual spot test. Strains were cultured to saturation in 2 ml YPD at 23°C, a six-fold dilution series generated and spotted onto YPD. Strains were incubated at the indicated temperatures for three days before being photographed. All plates contained the reference strains 640 (wild type), 1108 (<i>cdc13-1</i>) and 1412 (<i>yku70</i>Δ), indicated as red cultures in the key. The “Wild Type” single mutant strains assessed were: 6656, 6811, 3622, 3653, 6620, 1273, 659, 6862, 6927 6951, 6963, 6692 and 6632. The <i>cdc13-1</i> double mutant strains assessed were: 6810, 6814, 3624, 3655, 6614, 1296, 1258, 6860, 6928, 6865, 6967, 6694 and 6396. The <i>yku70</i>Δ double mutant strains assessed were: 6808, 6812, 4290, 4296, 6628, 1409, 1284, 2413, 2415, 6968, 6971, 6776 and 6763. Growth at other temperatures is shown in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen.1001362.s002\" target=\"_blank\">Figure S2</a>.</p>", "links"=>[], "tags"=>["interactions"], "article_id"=>455671, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Confirmation_of_genetic_interactions_in_an_alternative_genetic_background_/455671", "title"=>"Confirmation of genetic interactions in an alternative genetic background.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-07 01:34:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/785545"], "description"=>"<p>Disruption of NMD activity results in higher Stn1 transcript and protein levels (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001362#pgen-1001362-g005\" target=\"_blank\">Figure 5</a>). Stn1 promotes capping directly and is thought to oppose telomerase recruitment through interaction with Cdc13. Since telomerase has telomere capping function, Stn1 therefore both promotes and inhibits telomere capping.</p>", "links"=>[], "tags"=>["telomere", "capping", "activities", "influenced"], "article_id"=>455896, "categories"=>["Genetics", "Medicine"], "users"=>["Stephen Gregory Addinall", "Eva-Maria Holstein", "Conor Lawless", "Min Yu", "Kaye Chapman", "A. Peter Banks", "Hien-Ping Ngo", "Laura Maringele", "Morgan Taschuk", "Alexander Young", "Adam Ciesiolka", "Allyson Lurena Lister", "Anil Wipat", "Darren James Wilkinson", "David Lydall"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001362.g006", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_of_telomere_capping_activities_influenced_by_NMD_/455896", "title"=>"Model of telomere capping activities influenced by NMD.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-07 01:38:16"}

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