Ontology highlight
ABSTRACT:
PROVIDER: PRJNA610036 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11231052.fastq.gz | Fastqsanger.gz | |||
| SRR11231053.fastq.gz | Fastqsanger.gz | |||
| SRR11231054.fastq.gz | Fastqsanger.gz |
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Project description:We report DNA content of yeast strains that are growing asynchronously or treated with hydroxyurea (HU). We selected two strains from our Epi-Decoder library, that are wild-type but have BAR1 or RPO21 TAP-tagged. This reveals that HU-treated samples have peaks in DNA content representing stalled replication forks.
2018-07-16 | GSE114290 | GEO
Project description:Transcription of transfer-RNA genes (tDNAs) by RNA Polymerase III (RNAPIII) is tightly regulated upon nutrient and stress signaling. However, identical tDNAs across the genome are differentially regulated, suggesting regulation at the chromatin-level plays a crucial role. This study aimed to identify such mechanisms by decoding the chromatin proteome of a native tDNA locus in yeast using Epi-Decoder. The tDNA proteome showed dynamic binding of both known and unknown factors upon nutrient stress, including Ykr011c (Fpt1), a protein of unknown function. Decoding the tDNA proteome in the absence of Fpt1 revealed a role in the eviction of RNAPIII during repressed transcription. Fpt1 exclusively occupied RNAPIII-regulated genes, but cells without Fpt1 also showed impaired shutdown of RNAPII-transcribed ribosome biogenesis genes in changing nutrient conditions. These findings provide support for a novel chromatin-associated regulator required for proper RNAPIII assembly that also tunes an integrated physiological response to changing metabolic conditions.
2023-11-21 | GSE228556 | GEO
Project description:we examined the glycoproteomics of N-glycosylation in untreated LNCaP (NC), ST-EPI, LT-EPI, ST-ENZ, and LT-ENZ groups using Tandem Mass Tag (TMT) labels by nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS).LNCaP-NC, SP-EPI, SP-ENZ, LP-EPI, and LP-ENZ cells each with two biological replicates were used for glycoproteomics analysis.
2022-08-12 | PXD030036 | Pride
Project description:DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2) are important epigenetic repression marks for silencing transposons in heterochromatin and regulating gene expression in plant development. However, the mechanistic relationship to other repressive marks, such as histone H3 lysine 27 trimethylation (H3K27me3), is unclear. OsFIE1 (Fertilization Independent Endosperm 1) encodes an Esc-like core component of the Polycomb repressive complex 2 (PRC2), which is involved in H3K27me3-mediated gene repression. Here, we identify a gain-of-function epi-allele (Epi-df) of rice OsFIE1; this allele exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We found that Epi-df has no changes in its nucleotide sequence, but is hypo-methylated in the promoter and the 5' region of OsFIE1 and has reduced H3K9me2 and increased H3K4me3. In Epi-df, OsFIE1 was ectopically expressed and its imprinting status was disrupted. OsFIE1 interacted with rice E(z) homologs, consistent with its role in H3K27me3 repression. Ectopic expression of OsFIE1 in Epi-df resulted in alteration of H3K27me3 levels in hundreds of genes. Therefore, this work identifies a novel epi-allele involved in H3K27me3-mediated gene repression, that itself is highly regulated by histone H3K9me2, thereby shedding light on the link between two important epigenetic marks regulating rice development. We report the application of ChIP-Seq technology for high-throughput profiling of histone modifications in WT (wild type) and Epi-df (mutant). We demonstrate that the H3K27me3 status is perturbed at target genes and leads to mis-regulated expression in Epi-df.
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Project description:Here, we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq) offering both high sensitivity and high resolution.
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Project description:We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes. We used microarrays to identify differentially expressed genes in Epi-df. For genome-wide expression analysis of Epi-df, three replicates of WT and Epi-df samples (RNA from 3-week-old seedlings) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.
2012-07-12 | E-GEOD-39298 | biostudies-arrayexpress
Project description:Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epi-specific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation and repression of divergent transcriptional programs.
2021-07-30 | GSE181097 | GEO
Project description:Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epi-specific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation and repression of divergent transcriptional programs.
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