Genomic analysis of the scc2-4 mutant in budding yeast
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae BY4741
SUBMITTER: Musinu Zakari
PROVIDER: E-GEOD-55358 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients. One hypothesis is that, reduced binding of Scc2 causes gene misregulation. To further explore this idea ChIP-seq was performed using an scc2-4 mutant. We observed from the analysis, we observe reduce binding of Scc2 to Pol II transcribed genes (snoRNAs, ribosomal protein genes) and pol II transcribed genes (tRNAs). Studies are currently underway to examine the biological implications of this observation. Examining genome-wide binding of scc2-4 mutant
2015-06-16 | E-GEOD-55357 | biostudies-arrayexpress
Project description:The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients.This has led to the hypothesis that developmental disorders in CdLS patients are a result of dysregulated gene expression. To examine the transcriptional program of Scc2 mutants called scc2-4, RNA sequencing was performed. Analysis of gene expression program shows upregulation of genes involved in ribosome biogenesis and downregulation of genes needed for oxidative phosphorylation. Studies are currently underway to investigate how scc2-4 mutation causes gene misregulation. The answer(s) could provide insight into the molecular etiology of CdLS. Examining gene expression in 3 biological replicates of scc2-4 relative to wt by Ilumina sequencing
2015-06-16 | E-GEOD-55316 | biostudies-arrayexpress
Project description:The budding yeast E3 SUMO ligase Mms21, a component of the Smc5-6 complex, regulates sister chromatid cohesion, DNA replication, and DNA repair. We identify a role for Mms21 in ribosome biogenesis. The mms21RINGD mutant exhibits reduced rRNA production, nuclear accumulation of 60S and 40S ribosomal proteins, and elevated Gcn4 translation. Genes involved in ribosome biogenesis and translation are down-regulated in the mms21RINGD mutant. Examining gene expression profile of mms21RINGD mutant compared to wild-type by RNA Seq using Ilumina sequencing
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-04-03 | E-GEOD-54743 | biostudies-arrayexpress
Project description:Eco1 is an acetyltransferase subunit of the cohesin complex and acts during DNA replication to establish cohesion between sister chromatids. However, cohesin has additional functions in gene expression, DNA damage repair, and higher-order organization of chromosomes. The eco1 mutant W216G disrupts acetyltansferase activity, and causes genome-wide transcriptional defects which can be suppressed by deletion of FOB1, a gene also involved in DNA replication. This experiment investigates gene expression differences between the eco1-W216G mutant, and mutants in FOB1, and RAD61 a gene involved in inhibition of cohesion establishment but mutation of which is able to suppress temperature sensitivity of the eco1-W216G mutant. Wt and mutant strains of yeast were grown to mid log phase in liquid culture in triplicate and harvested for comparison on Affymetrix microarrays. The following strains were compared: 1) eco1-W216G, 2) eco1-W216G fob1Δ, 3) eco1-W216G rad61Δ, 4) fob1Δ, 5) rad61Δ, and 6) WT.
2014-04-03 | E-GEOD-54741 | biostudies-arrayexpress
Project description:The cohesin protein complex is well known for playing a role in chromosome segregation. However, it has additional less understood roles in transcription, DNA repair, and chromosome condensation. Mutants in two yeast orthologues (Eco1 and Scc2) of human cohesinopathy disease alleles were examined by transcriptional profiling in response to perturbation of the transcriptional program by amino acid starvation. Two cohesin mutants were compared to wt in a time course of amino acid starvation consisting of 4 time points, 3 replicates of each, for a total of 36 samples.
2011-04-01 | E-GEOD-27235 | biostudies-arrayexpress
Project description:A Candida glabrata wild type strain (HTL, as described in Schwartzmuller et al., PLoS Pathog. 2014 Jun 19;10(6):e1004211) was submitted to various stress conditions (iron excess, salt excess, cadmium treatment and iron starvation (BPS treatment). The cells were collected 20 and 40 minutes after the beginning of treatments and their transcriptomes were compared to those of mock treated cells.
2018-11-12 | E-MTAB-7043 | biostudies-arrayexpress
Project description:To measure the impact of Hap5 regulation on its targets, we performed transcriptome analyses comparing gene expression in a hap5 deletion mutant and in wild type cells. Because our ChIP-seq results showed an interaction between Hap5 and the targets of Yap5, we performed these transcriptome experiments on cells grown in three different conditions: standard rich media, iron excess and iron starvation.
2017-03-31 | E-MTAB-5348 | biostudies-arrayexpress
Project description:Gene expression was compared for wild type yeast (BY4741) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3â strain. The gal11-myc allele shows a partial loss of function when combined with med3â. Expression was analyzed for yeast grown in YPD as well as in CSM. We also examined gene expression of the wild type strain BY4742 grown in YPD and include that data here. Gene expression was compared for wild type yeast (BY4741 and BY4742) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3â strain.
2011-08-31 | E-GEOD-31774 | biostudies-arrayexpress
Project description:Eco1 is the acetyltransferase that establishes sister-chromatid cohesion during DNA replication. Budding yeast with an eco1 mutation that genocopies Roberts syndrome displaysreduced ribosomal DNA (rDNA) transcription and a transcriptional signature of starvation. Weshow that deleting FOB1, a gene encoding a specific replication fork blocking protein for therDNA region, rescues rRNA production and partially rescues transcription genome-wide. This experiment examines the effect of eco1 mutation on replication genome-wide. Furtherstudies show that deletion of FOB1 corrects the genome-wide replication defects, nucleolarstructure, and rDNA segregation in an eco1 mutant. Our study highlights cohesin's central role atthe rDNA for global control of DNA replication and gene expression. DNA content in eco1-W216G mutant and wt yeast is measured in duplicate by sequencing at 0, 20, and 40 minutes following release from G1 arrest.
2014-04-03 | E-GEOD-54742 | biostudies-arrayexpress