Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq facilitates the quantitative analysis of Rvb proteins' enrichment on the genome during stress

ABSTRACT: The goals of this study are to quantitatively analyze the enrichment of Rvb1/Rvb2 on the yeast genome during glucose starvation. The ChIP-seq files were generated from 2 biological replicates of Rvb1’s immunoprecipitation (IP), Rvb2-IP, and Pgk1-IP in 10-min glucose starved yeast cells, respectively, using NextSeq 500 SR 75. The sequence reads that passed quality filters were analyzed by calculation of the read counts on 2 regions: -500 bp to TSS and TSS to +500 bp. Using an optimized data analysis workflow, we found Rvb1/Rvb2’s enrichment peaks and that they are significantly more enriched on the Class II alternative glucose metabolism promoters than Class I heat shock promoters.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE184473 | GEO | 2021/09/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Structure of transcription preinitiation complex engaged with the +1 nucleosome

Project description:The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles in chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is positioned downstream of the core promoter. Here we present the cryo-EM structure of the yeast PIC bound to promoter DNA and the +1 nucleosome at a resolution of 3.4–3.9 Å. The general transcription factor TFIIH forms four contacts with the nucleosome, indicating how PIC assembly can be assisted by the +1 nucleosome. The TFIIH subunit Ssl2 (XPB in human TFIIH) forms a wedge between promoter DNA and the nucleosome, stabilizing two turns of DNA that are detached from the nucleosome. During subsequent scanning for the transcription start site (TSS), three additional turns of DNA can be detached before the partially unraveled nucleosome may counteract further scanning, explaining why TSSs are located at a distance of ~60 bp from the dyad of the +1 nucleosome in yeast.

2023-03-11 | PXD029840 | Pride

Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (ChIP-Seq)

2013-09-04 | GSE50551 | GEO

Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (ChIP-Seq)

Project description:ChIP-Seq analysis revealed that suberoylanilidehydroxamic acid (SAHA) increases genome-wide H4 acetylation in differentially regulated genes, except for the 500 bp upstream of transcription start sites (TSS). Chromatin immunoprecipitation (ChIP) with massively parallel high throughput sequencing (Seq) was used to map genome-wide histone H4 acetylation (K4/7/11/15) in the presence or absence of SAHA in differentiating MC3T3 sc4 osteoblasts.

2013-09-04 | E-GEOD-50551 | biostudies-arrayexpress

Genome-wide high resolution map of transcription start sites across the life cycle of Oikopleura dioica

Project description:The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. TSS selection grammars include a genome-wide shift during spermatogenesis to promoters with a novel, position-specific, core promoter element, present in >70% of male-specific promoters. Differential promoter usage in spermatogenesis includes the activation of cryptic internal promoters within polycistronic operons, alternative TSS selection within promoters of genes expressed in earlier development and the exclusion of trans-splice sites. In contrast, maternal promoters, which are active in endocycling nurse nuclei in O. dioica, lack position-specific motifs, have dispersed TSS usage, ordered nucleosomes around the TSS and typical histone modifications associated with broad promoters. Furthermore, our results indicate that the cell cycle regulator, E2F1, acts as a master regulator of these maternally expressed genes. Zygotic promoters are also predominantly broad and the vertebrate maternal to zygotic switch in mode of TSS-selection is absent. DNA methylation in gene bodies is an ancient property of eukaryotic genomes and is thought to repress alternative TSSs. We report a strong association between gene body DNA methylation, H3K4me3-depletion and TATA-dependent sharp promoters in O. dioica. Core promoter features may therefore determine the subset of gene bodies that are methylated in this invertebrate genome.

2018-02-05 | GSE78794 | GEO

Large-scale interactome screen for predicted transcription factors in fission yeast using IP-MS.

Project description:Large-scale interactome screen for 89 transcription factors (TFs) in fission yeast. TFs are tagged at the endogenous locus with a 3xFLAG affinity epitope. Cells cultured under optimal conditions (30°C, rich medium) were subjected to IP-MS at 150 mM an 500 mM NaCl.

2024-08-30 | PXD054070 | Pride

Dependency of Gene Expression in Saccharomyces cerevisiae on extracellular Glucose Concentration

Project description:The goal of this study is to analyse how the gene expression in Saccharomyces cerevisiae changes in dependency on the glucose concentration. Therefore, fed batch cultivations were carried out, during which the glucose concentration was maintained stable for several hours. Samples were taken at different times during the cultivations, the RNA was isolated and hybridised on whole genome yeast microarrays. Results from cultivations with the glucose concentrations 50, 70, 100 and 500 mg/L are presented. In addition, one sample from a starvation period (0 mg/L glucose) was analysed. Keywords: Dependency on glucose concentration

2007-12-02 | GSE6358 | GEO

The evolution, evolvability, and engineering of gene regulatory DNA [GPRA]

Project description:In order to generate data produce a generalizable sequence-to-expression model, we randomly sampled ~21 million 80 bp sequences and tested their activity as promoters (in yeast) by measuring expression level by FACS (sorting into 18 bins).

2021-12-23 | GSE163045 | GEO

Selection of yeast Saccharomyces cerevisiae promoters available for xylose cultivation and fermentation

Project description:To select candidate promoters that function in the presence of xylose, we performed comprehensive gene expression analyses using xylose-utilizing yeast strains both during xylose and glucose fermentation.

2017-04-11 | GSE97580 | GEO

Ab initio identification of transcription start sites (TSSs) in the Rhesus macaque genome by histone modification and RNA-Seq

Project description:We addressed the lack of experimentally supported transcript annotations in the Rhesus macaque genome by ab initio identification of the transcription start sites (TSSs). We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark TSSs and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures in the macaque brain. We then integrated the two types of our newly generated data with genomic sequence features and extended a TSS prediction algorithm to ab initio predict and verify 16,833 of previously electronically annotated transcription start sites at 500 bp resolution and predicted ~10,000 new TSSs.

2010-10-19 | GSE24538 | GEO

Genome-wide distribution of proteins Pita, ZIPIC, Zw5 in Drosophila embryos

Project description:According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer–promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita, and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to promoters near the TSS. They are structurally similar in containing the N-terminal zinc finger-associated domain (ZAD) and different numbers of C2H2-type zinc fingers at the C-terminus. We have shown that the ZAD domains of ZIPIC, Pita, and Zw5 usually form homodimers. In Drosophila transgenic lines, these proteins can support long-distance interaction between GAL4 activator and the reporter gene promoter. However, no functional interaction between binding sites for different proteins has been revealed, suggesting that such interactions are highly specific. ZIPIC facilitates long-distance stimulation of reporter gene by GAL4 activator in yeast. Thus, ZAD-containing zinc-finger proteins probably belong to the class of architectural proteins.

2016-05-06 | GSE76997 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data