Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1055295 | ENA |
REPOSITORIES: ENA
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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: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.
2013-12-04 | E-GEOD-40674 | biostudies-arrayexpress
Project description:Here, we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq) offering both high sensitivity and high resolution.
2023-07-11 | GSE235896 | GEO
Project description:In this study, we engineered a micro-well duct-on-chip platform to generate defined 3D aggregates from hiPSC-derived PPs and subsequently induce differentiation toward PDLOs. Time-resolved scRNA-seq combined with cleared immunofluorescence imaging provided a deep understanding of in vitro ductal cell type differentiation. By defining the emergent cell types at each stage of differentiation based on their gene expression profiles and organoid structures, we provide a precise cell-by-cell description of the in vitro differentiation trajectory. Transcriptional data of PDLOs were complemented by their proteome and secretome data, allowing the identification and validation of prognostic cancer marker. Thus, we show the applicability of hiPSC-derived PDLOs-on-chip for future ductal disease modeling.
2021-07-08 | PXD024461 | Pride
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:RUVBL2 is most important AAA+ ATPase for RNA polymerase II assembly and transcription regulation, through DNA remodeling or by directly interaction with PIC，this study will comprehensively to study the promiscuous functions of this proteins through the ChIP-MS, ChIP-seq, RNA-seq and nascent RNA seq and biochemistry analysis. Our study would provide more systematic and novel responsibility of this molecule, especially for the development and carcinomas.
2022-09-29 | PXD036528 | Pride
Project description:Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful tool to dissect global epigenetic landscapes of cells. However, this method usually consumes millions of cells. Here we develop a robust technique for performing ChIP-Seq using as low as 1,000 cells. This method combines a semi-automatic nanoliter ChIP reaction with a carrier-based sequencing library preparation strategy without pre-amplifying the ChIP product. We used this method to investigate the pattern of trimethylation of histone 3 lysine 4 (H3K4me3) of mouse post-implantation epiblast cells at embryonic day 6.5 (E6.5) and showed that it is more similar to that of mouse Epi-Stem cells (mEpiSCs) than that of mouse Embryonic Stem cells (mESCs). Together with the high similarity between the transcriptomes of EpiSCs and E6.5 epiblast cells, this suggests that mEpiSCs is a reliable in vitro model for post-implantation epiblast cells in vivo. Use 1 million mEpiSCs and 1million mESCs as the positive control, 1000 mEpiSC and 1000 mESCs samples are used to validate the protocol. 1000 mEpiblasts have two biological replicates
2015-07-24 | E-GEOD-59738 | biostudies-arrayexpress
Project description:Transcription factor/enhancer interactions determine cell specific gene expression. Here, we followed enhancers during differentiations of embryonic stem (ESCs) to epiblast like cells (EpiLCs). There were highly dynamic changes in histone lysine 27 acetylation at enhancer sites throughout the genome. These sites were enriched for a Foxd3 binding motif, a forkhead transcription factor essential in early embryonic development. Surprisingly, Foxd3 occupied largely mutually exclusive sites in the ESCs versus EpiLCs. Foxd3 bound to nucleosome occupied regions, simultaneously evicting the histones while inhibiting full gene expression through the recruitment of histone deacetylases. Knockout of Foxd3 resulted in hyperacetylation and transcriptional upregulation of neighboring genes, many of which were further upregulated at later stages of differentiation. These data show that Foxd3 primes enhancer sites during pregastrulation by removing nucleosomes, yet suppresses neighboring histone hyperacetylation. Such a mechanism may be common to many transcription factors that prepare enhancers for later gene activation during development. ChIP-seq of H3K4me1, H3K27ac, H3K27me3, p300, H3K4me3, RNA Pol2 and Oct4 in four pluripotent states: embryonic stem cells (ESCs) day 1 ESC differentiation, Epi-like stem cells (EpiLCs), and epiblast stem cells (EpiSCs); ChIP-seq of 3XFlag tagged Foxd3 in ESCs and EpiLCs; ChIP-seq of H3K4me1, H3K27ac, H3K27me3, p300 and H3K4me3 in Foxd3 conditional knockout cells (tamoxifen-inducible) -/+ 36h Tamoxifen treatemnt. ChIP seq of Flag-Foxd3 (third replicate), ChIP-seq of HDAC1 and Brg1 in WT and Foxd3 KO cells and MNase-ChIP-seq of H3K4me1
2015-12-08 | E-GEOD-58407 | biostudies-arrayexpress