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K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

ABSTRACT: 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.

ORGANISM(S): Kluyveromyces lactis

PROVIDER: GSE65792 | GEO | 2015/07/06

SECONDARY ACCESSION(S): PRJNA275069

REPOSITORIES: GEO

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K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

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

2015-07-06 | E-GEOD-65792 | biostudies-arrayexpress

ChIP-Seq of constitutively expressed Ndt80-Myc in K. lactis

Project description:The purpose of this experiment was to identify the genes bound by Ndt80 in K. lactis when constitutively expressed. Ndt80 was tagged with c-myc, the native Ndt80 promoter was replaced with the K. lactis Gal1 promoter and the protein was immunoprecipitated with a c-myc antibody. Cells were grown overnight in SRaffinose until log-phase, then in SRaffinose + 1.7% Galactose for 5 hours. Each experiment was repeated twice and sequenced on an Illumina HiSeq 4000.

2017-05-01 | GSE90662 | GEO

Kluyveromyces lactis

Project description:K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

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ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1)

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. 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.

2010-12-01 | E-GEOD-25209 | biostudies-arrayexpress

Functions of STE12 in Trichoderma reesei

Project description:We investigated the function of the transcription factor STE12 and found an involvement in gene expression and growth in light and darkness

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Genome-wide Ste12-binding site mapping in MATa segregants of YJM789 x S96 cross

Project description:In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. We showed that the majority of TF binding variation is cis-linked and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several known and proposed Ste12 cofactors. We also identified two trans factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than 10 genes under Î±-factor treatment. Neither of these two genes was known to regulate Ste12 previously, and we suggest that they may be key mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes indicating that binding variation is functional. Many of the variable bound genes are involved in cell wall organization and biogenesis. Overall, we identified key regulators of molecular diversity among individuals and provide novel insights into mechanisms of gene regulation. Two ChIP-Seq experiments and one Input DNA-Seq experiment for the yeast strains S96, HS959 and 43 MATa segregants were performed under alpha factor treatment conditions; an additional replicate was also performed for some of the strains. One ChIP-Seq experiment for each parental strain was performed without alpha factor treatment, and one ChIP-Seq experiment for each of the 24 deletion strains was performed under alpha factor treatment.

2010-02-18 | E-GEOD-19635 | biostudies-arrayexpress

Genome-wide Ste12-binding site mapping in MATa segregants of YJM789 x S96 cross

Project description:In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. We showed that the majority of TF binding variation is cis-linked and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several known and proposed Ste12 cofactors. We also identified two trans factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than 10 genes under α-factor treatment. Neither of these two genes was known to regulate Ste12 previously, and we suggest that they may be key mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes indicating that binding variation is functional. Many of the variable bound genes are involved in cell wall organization and biogenesis. Overall, we identified key regulators of molecular diversity among individuals and provide novel insights into mechanisms of gene regulation.

2010-02-18 | GSE19635 | GEO

Transcription profiling of S. cerevisiae haploid Sigma1278b strains expressing different combinations and variants of TEC1 and STE12

Project description:We determined and classified Tec1-regulated genes in haploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of five different haploid MATa yeast strains of the following relevant genotypes: (53 = YHUM1694) TEC1 STE12; (64 = YHUM1700) tec1? STE12; (66 = YHUM1701) tec1? ste12?; (10 = YHUM1676) (P)URA3-TEC1 ste12?; (42 = YHUM1642) (P)URA3-TEC1 1-280-STE12 1-688 tec1? ste12?. All strains were grown in duplicate in SC medium lacking leucine and histidine at 30 degree C to an optical density of 1.0 before extraction of total RNA and transcriptional profiling.

2010-05-22 | E-MEXP-2207 | biostudies-arrayexpress

Lactococcus lactis MG1363 ∆guaA versus L. lactis MG1363 (wt)

Project description:Gene expression in Lactococcus lactis MG1363 was compared to that of L. lactis MG1363 ∆guaA in rich GM17 medium.

2016-01-12 | GSE76764 | GEO

Response of L. lactis faced to S. cerevisiae

Project description:The response of L. lactis to the presence of S. cerevisiae was analyzed during the exponential growth phase in fermentors in defined growth conditions. Although no growth kinetic difference was observed between the pure and mixed culture of L. lactis, the mRNA level of genes was significantly modified. More particularly, a strong reorientation of pyrimidine metabolism was observed when L. lactis was grown in the mixed culture. Keywords: microbial interaction, time course A pure culture of L. lactis was conducted in parallel with a co-culture of L. lactis and S. cerevisiae. For the transcriptomic analysis, the mixed culture (test condition, 2.5 hours of culture, Bâ) was compared to the pure culture (reference, 2.5 hours of culture, B) on the same slide at the same time. The mRNA level changes between 2 and 3 hours (A and C samples) flanking B sample (2.5 hours) in the pure culture were also determined on another slide. Total RNA was extracted from these samples and labelled cDNA (Cy3/Cy5) were prepared and hybridized on glass slides exhibiting 2004 amplicons specific of Lactococcus lactis IL1403 genes. 3 independent repetitions were performed.

2010-05-18 | E-GEOD-9436 | biostudies-arrayexpress

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