Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA338171 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Nucleosome occupancy microarray for WT and jhd2-delete strains though sporulation
| PRJNA176158 | ENA
Project description:Affymetrix custom RNA microarray for WT and jhd2-delete strains in terminal spores (20h)
| PRJNA176159 | ENA
Project description:By using of paired-end sequencing technology, we report the high-throughput profiling of Jhd2 targeting in S. cerevisiae. We obtained more than 1.8E+7 Illumina reads and generated 1.1E+7 mapped reads from Jhd2-ChIP DNA . Sequence reads for Jhd2-ChIP and Input DNA were mapped to yeast genome by using the BWA (Burrows Wheeler Aligner), SAMtools (Sequence Alignment Map) programs and followed by SICER (Spatial clustering for Identification of ChIP-Enriched Regions) program to obtain the Significant peaks. We found that the overall Jhd2 distribution across the gene body of targets is fairly correlated to the levels of H3K4 di- and tri-methylation, which are enriched at 5’ through 3’ of ORF regions. These observations demonstrate that the Jhd2, a histone H3K4 demethylase, is linked to gene transcription by locating mainly at the coding regions to balance the H3K4me of its target genes at steady state. Furthermore, we observed that Jhd2 are significantly enriched at several specific chromosomal loci including telomeres, centromeres, silent HM loci, LTR-tRNAs, and rDNA arrays. Our study demonstrated that Jhd2, H3K4-demethylase, plays a dynamic role as a chromatin insulator to define boundary regions between euchromatin and heterochromatin by association with specific chromatin loci in the yeast genome.
2017-02-20 | GSE55281 | GEO
Project description:Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. However, how cells transduce nutrient availability to appropriate gene expression response via histone modifications remains poorly understood. Here, we report that glycolysis promotes H3K4me3 by activating Tpk2, the catalytic subunit of protein kinase A (PKA) via the Ras-cyclic AMP (cAMP) pathway. Further study showed that Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at S321 and S340 in response to glucose availability.Mechanistically, Tpk2-catalyzed Jhd2 phosphorylation inhibits its overall binding to chromatin and promotes its polyubiquitination by the E3 ubiquitin ligase Not4 and degradation by the proteasome. In addition, Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14ac by preventing the binding of Rpd3 to chromatin. By inhibiting the activity of Jhd2 and Rpd3, Tpk2-catalyzed Jhd2 phosphorylation regulates gene expression and promotes autophagy. Thus, regulation of Jhd2 by the Ras-cAMP-PKA pathway shed lights on how cells rewire their biological responses to glucose availability.
2022-08-29 | GSE175868 | GEO
Project description:Low level of H3 Lys4 tri-methylation is a signature feature of silenced chromatin regions. We used microarray to analyze the contribution of S. cerevisiae H3 Lys4 demethylase Jhd2p in silenced chromatin formation process. Total RNA from two JHD2 gene altered strains : jhd2 deletion and JHD2 over-expression, together with a set1 deletion strain (Set1p: H3 Lys4 methlase) were analyzed with Affymetrix Yeast 2.0 array. We sought to dissect Jhd2p functions into H3 Lys4 methylation related and unrelated parts by comparing microarry results of JHD2 and SET1 gene altered strains.
2015-12-31 | E-GEOD-33077 | biostudies-arrayexpress
Project description:Histone H3 lysine 4 tri-methylation (H3K4me3) is a hallmark of transcription initiation, but how H3K4me3 is demethylated during gene repression is poorly understood. Jhd2, a JmjC domain protein, was recently identified as the major H3K4me3 histone demethylase (HDM) in S. cerevisiae. While JHD2 is required for removal of methylation upon gene repression, deletion of JHD2 does not result in increased levels of H3K4me3 in bulk histones, indicating that this HDM is unable to demethylate histones during steady state conditions. In this study, we showed that this was due to the negative regulation of Jhd2 activity by histone H3 lysine 14 acetylation, which co-localizes with H3K4me3 across the yeast genome. We demonstrated that loss of the histone H3-specific acetyltransferases (HATs) resulted in genome-wide-depletion of H3K4me3, and this was not due to a transcription defect. Moreover, H3K4me3 levels were reestablished in HAT mutants following loss of JHD2, which suggested that H3-specific HATs and Jhd2 served opposing functions in regulating H3K4me3 levels. We revealed the molecular basis for this suppression by demonstrating that histone H3K14 acetylation negatively regulated Jhd2 demethylase activity on an acetylated peptide in vitro. These results revealed the existence of a general mechanism for removal of H3K4me3 following gene repression. Examination of H3K4me3 in WT, ada2sas3, ada2sas3jhd2, and jhd2 strains.
2012-11-05 | E-GEOD-41424 | biostudies-arrayexpress
Project description:Pre-mRNA splicing is vital for the proper function and regulation of eukaryotic gene expression. Saccharomyces cerevisiae has been used as a model organism for studies of RNA splicing because of the striking conservation of the spliceosome and its catalytic activity. Nonetheless, there are relatively few annotated alternative splice forms, particularly when compared to higher eukaryotes. Here, we describe a method to combine large scale RNA sequencing data to accurately discover novel splice isoforms in Saccharomyces cerevisiae. Using our method, we find extensive evidence for novel splicing of annotated intron-containing genes as well as genes without previously annotated introns and splicing of transcripts that are antisense to annotated genes. By incorporating several mutant strains at varied temperatures, we find conditions which lead to differences in alternative splice form usage. Despite this, every class and category of alternative splicing we find in our datasets is found, often at lower frequency, in wildtype cells under normal growth conditions. Together, these findings show that there is widespread splicing in Saccharomyces cerevisiae.
2024-05-01 | GSE120497 | GEO
Project description:We describe the landscape of H3K4me3 in WT and jhd2Î? cells in YAR media by ChIP seq To determine the contribution of Jhd2 to the H3K4me3 landscape in respiring yeast cells, we performed H3K4me3 ChIP and normalized to pan-H3 ChIP signal.
2016-08-09 | E-GEOD-85320 | biostudies-arrayexpress
Project description:Histone H3 K36me3 in wildtype, isw1 and chd1 yeast strains
| PRJNA154911 | ENA
Project description:Comparative Genomic Hybridization of natural Saccharomyces cerevisiae strains vs lab reference strains.
2020-12-31 | GSE136466 | GEO