Affymetrix custom RNA microarray for WT and jhd2-delete strains in terminal spores (20h)
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE41002 | GEO | 2012/10/01
SECONDARY ACCESSION(S): PRJNA176159
REPOSITORIES: GEO
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Project description:RNA transcript signals were profiled in WT (MMY718) and jhd2M-bM-^HM-^F (MMY1879) terminally sporulated cultures (20h of sporulation) using Affymetrix high resolution tiling microarrays. Total RNA was isolated, biotin labelled, and hybridized to custom Affymetrix Scerevisiae_tlg tiling arrays. The array contains 25nt probes covering the Watson strand of the yeast genome with 8nt tiling resolution, and another set of 25nt probes covering the Crick strand with 8nt resolution, with a 4nt offset from the Watson probes. This gives an overall tiling resolution of 4bp with a total of 6.5 million probes, and also allows detection of strand-specific RNA signals.
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Project description:WT (MMY718) and jhd2M-bM-^HM-^F (MMY1879) sporulating cell cultures were profiled for global nucleosome occupancy using Affymetrix high-resolution tiling arrays. MNase-treated mono-nucleosomes from WT and jhd2M-bM-^HM-^F cultures in rich media, and sporulation timepoints at 0h, 4h, 6h, 8h, 10h, 12h, and 16h were microarrayed.
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Project description:This work uncovers a novel and biologically significant mechanism that directly connects nutrient availability to histone modifications and gene transcription. We report that glycolysis promotes histone H3K4 trimethylation (H3K4me3) by activating Tpk2, a catalytic subunit of protein kinase A (PKA) via the Ras-cyclic AMP (cAMP) pathway. Glucose-activated PKA (Tpk2) inhibits Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at serine 321 and serine 340. In addition, Tpk2- catalyzed Jhd2 phosphorylation promotes H3K14ac by preventing the binding of Rpd3 at chromatin.
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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.
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Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylation−demethylation control chromatin dynamics during various facets of transcriptional regulation.
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2016-06-15 | GSE81022 | GEO
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylationâdemethylation control chromatin dynamics during various facets of transcriptional regulation. Genome-wide nucleosome maps were generated from three different yeast strains representing wild type control, set1 null and jhd2 null mutants. Three independent biological samples were grown for each strain, nucleosomes were prepared by micrococcal nuclease digestion, libraries were prepared, mononculeosomal DNA was isolated, sequenced, and analyzed separately.
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