Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq of Fragaria.vesca

ABSTRACT: Histone modifications mediate between genes and environment in plant growth and developmental events. To characterize the histone modification signatures in strawberry, we performed ChIP-seq experiments for seven histone marks in the immature and mature fruits, and leaves of the woodland strawberry F. vesca ('Ruegen'). The seven histone marks include H3K9/K14ac, H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3 and H3K9me2. In addition, to reveal the effect of the histone deacetylase FvHDA6, H3K9/K14a was profiled in FvHDA6-OE fruits.

ORGANISM(S): Fragaria vesca

PROVIDER: GSE208638 | GEO | 2024/09/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila

Project description:In Drosophila the chromosomal kinase JIL-1 is responsible for most interphase histone H3S10 phosphorylation and has been proposed to protect active chromatin from acquiring heterochromatic marks, like dimethylated histone H3K9 (H3K9me2) and HP1. Here, we show that JIL-1’s targeting to chromatin depends on a PWWP domain-containing protein JASPer (JIL-1 Anchoring and Stabilizing Protein). The JASPer-JIL-1 (JJ)-complex is the major form of the kinase in vivo and is targeted to active genes and telomeric transposons via binding of the PWWP domain of JASPer to H3K36me3 nucleosomes, where the complex modulates the transcriptional output. JIL-1 and JJ-complex depletion in cycling cells lead to small changes in H3K9me2 distribution at active genes and telomeric transposons. Finally, we identify several interactors of the endogenous JJ-complex and propose that JIL-1 not only prevents heterochromatin formation but also coordinates chromatin-based regulation in the transcribed part of the genome.

2019-10-09 | PXD012790 | Pride

Analysis of histone methylation in the neocortex of Phf8 KO mice [ChIP-seq]

Project description:Phf8 is a histone demethylase with links to human behavior. To gain insight into Phf8's function in the brain, we have performed ChIP-seq for the histone methylation marks H3K4me3, H3K4me1, H3K27me2 and H3K9me2.

2017-02-14 | GSE90018 | GEO

Refined read-out: hUHRF1‑tandem Tudor prefers histone H3 containing K9me2/3 and K4me1

Project description:Histone post-translational modifications (PTMs) are an important part of chromatin signaling mechanisms. Among them, histone H3 has a prominent role, and combinations of multiple PTMs are common. We investigated binding of multiple marks on the same H3 histone by the human UHRF1-TTD (Uniprot Q96T88, residues 126-280), known to bind H3K9me2/3 histones. We verified binding to H3K9me2/3 and demonstrated stronger binding to synthetic H3 peptides containing K4me1 and K9me2/3 as well as native HepG2 mononucleosomes bearing both H3K9me2/3 and H3K4me1.

2023-08-11 | GSE213741 | GEO

Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in PlantsM-BM-

Project description:DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2 and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homologue, ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both BAH and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes, and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains, and reveals a novel mechanism of interplay between DNA methylation and histone modification. Investigation of genome-wide occupancy of CMT3 by ChIP-seq

2012-11-11 | E-GEOD-39097 | biostudies-arrayexpress

Histone modifications in the marine diatom Phaeodactylum tricornutum

Project description:Genome wide mapping of five histone marks (H3K4me2, H3K9me2, H3K9me3, H3K27me3 and H3AcK9/14) as well as nucleosome occupancy was generated by chromatin immunoprecipitation followed by deep sequencing. To gain insights into the dynamic nature of the P. tricornutum epigenome in response to an environmental cue, we analyzed the impact of nitrate depletion. We specifically examined three histone modifications (H3K4me2, H3K9/14Ac and H3K9me3) using Chip-seq. Examination of 5 different histone modifications.

2015-05-05 | E-GEOD-68513 | biostudies-arrayexpress

Genome-wide maps of chromatin state in human iPSC derived Cardiomyocytes with 2N and 4N DNA content.

Project description:ChIP-seq was performed for seven marks (H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K27me3, H3K9me3, and H3K36me3) with Inputs on iPSC derived Cardiomyocytes with either 2N or 4N DNA content (3 replicates). Replicates were combined and put into the ChromImpute and ChromHMM pipelines (Ernst and Kellis, 2015), and a 25 state chromatin profilefor each was developed.

2021-05-06 | GSE130285 | GEO

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

Project description:Heterochromatin is a tightly packed form of DNA, which is associated with histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2 binding protein, Agenet domain (AGD)-containing protein 1 (AGDP1), in Arabidopsis thaliana. Our biochemical studies revealed that the AGDP1 can specifically recognize the H3K9me2 marks by the three pairs of tandem-AGDs. We determined the crystal structure of the AGD12 of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 employs a newly defined interacting interface to specifically recognize the H3K4me0 and H3K9me2 marks. In addition, we found that AGDP1 is required for transcriptional gene silencing, non-CG DNA methylation, and H3K9 dimethylation. Our ChIP-seq data showed that AGDP1 is enriched in TE regions and associated with the heterochromatin marks. Our findings suggest that, as a heterochromatin binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.

2018-10-23 | GSE111609 | GEO

H3K9 methylation regulates heterochromatin silencing through incoherent feedforward loops

Project description:Histone H3 lysine-9 methylation (H3K9me) is a hallmark of the condensed and transcriptionally silent heterochromatin. It remains unclear how H3K9me controls transcription silencing and how cells delimit H3K9me domains to avoid silencing essential genes. Here, using Arabidopsis genetic systems that induce H3K9me2 in genes and transposons de novo, we show that H3K9me2 accumulation paradoxically also causes the deposition of the euchromatic mark H3K36me3 by a SET domain methyltransferase, ASHH3. ASHH3-induced H3K36me3 confers anti-silencing by preventing the demethylation of H3K4me1 by LDL2, which mediates transcriptional silencing downstream of H3K9me2. These results demonstrate that H3K9me2 not only facilitates but orchestrates silencing by actuating antagonistic silencing and anti-silencing pathways, providing insights into the molecular basis underlying proper partitioning of chromatin domains and the creation of metastable epigenetic variation.

2024-06-27 | GSE246527 | GEO

Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in Plants

2012-11-11 | GSE39097 | GEO

Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases

Project description:Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. We investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of five H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. H3K9me2 was regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments were regulated by different MTases. H3K9me2 in A compartments was primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments was regulated by all five MTases. Furthermore, decreased H3K9me2 correlated with changes to the more active compartmental state that accompanied transcriptional activation.

2021-08-05 | PXD024756 | Pride

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