ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1)
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ABSTRACT: ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1). The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein. For the RME1 ChIPs, the cells grown with out phosphate. For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD. Epitope tagged strains were compared to untagged control strains. Two biological replicates were preformed for the RME1 ChIP. For the MATa1 and MATalpha2 ChIP, peaks were considered indicative of binding if both MATa1 and MATalpha2 showed enrichment above the untagged control.
Project description:ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1). The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein. For the RME1 ChIPs, the cells grown with out phosphate. For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD.
Project description:The mammalian gastrointestinal tract and the bloodstream are highly disparate biological niches, and yet certain commensal-pathogenic microorganisms are able to thrive in both environments. Here, we report the evolution of a unique transcription circuit in the yeast, Candida albicans, which determines its fitness in both host niches. Our comprehensive analysis of the DNA-binding proteins that regulate iron uptake by this organism suggests the evolutionary intercalation of a transcriptional activator called Sef1 between two broadly conserved transcriptional repressors, Sfu1 and Hap43. The Sef1 activator of iron uptake genes promotes virulence in a mouse model of bloodstream infection, whereas the Sfu1 repressor is dispensable for virulence but promotes gastrointestinal commensalism. We propose that the ability to alternate between genetic programs conferring resistance to iron depletion in the bloodstream versus iron toxicity in the gut may be a fundamental attribute of gastrointestinal commensal-pathogens. ChIP analyses to profile genome-wide of distribution of Sef1, Sfu1 and Hap43 in response to various iron availability. 12 independent ChIP experiments were performed on 6 biological replicates of the untagged control and 2 biological replicates each of Sef1-Myc, Sfu1-Myc, and Hap43-Myc.
Project description:The Zap1 ChIP-chips were performed in a/alpha cell types using C-terminally Myc-tagged proteins and Myc antibodies. ChIPs were performed on 48 hour biofilm cells grown in Spider medium. Two biological replicates were performed, and normalized data is reported in matrix. Myc tagged strains were compared to untagged control strains.
Project description:The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting. A control untagged strain was processed in parallel. The experiment was repeated 3 times, and sequenced on an Illumina HiSeq 2500. K. lactis Ste12-myc vs. untagged control under pheromone response condition with 3 technical replicates done on different days
Project description:The planktonic versus biofilm gene expression arrays were performed in a/alpha cell types. Gene expression arrays were performed on planktonic vs biofilm cells grown in Spider medium at 37C. Normalized data is reported in matrix. Biofilm strains (48 hour biofilms) were compared to planktonic strains (log phase planktonic cells) in Spider medium at 37C.
Project description:We examine how different transcriptional network structures can evolve from an ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species. Six samples were analyzed, three of which were controls and three of which were experimental
Project description:Control ChIP-seq matched with ChIP-seq on human K562 eGFP-tagged transcription factors. The White lab used goat anti-GFP antibody to perform ChIP in untagged K562 cells as a background control. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:Yeast strains expressing either GST-tagged or untagged Ypt1 were grown in either normal media or in media treated with 10mM DTT, to induce UPR A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. GeneticModification: GST tagged/untagged YPT1 Media: DTT present/absent in media