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MetabolomicsDisruption of Methionine Metabolism Drives Erythroid Cell Fate Reprogramming by Remodeling the H3K4me3 Landscape

Methionine cycle plays critical roles in cell fate determination by shaping epigenetic landscape, yet its function in human erythropoiesis remains undefined. Here, we show that disruption of methionine metabolism by compromising key enzyme adenosylhomocysteinase (AHCY) reshapes H3K4me3 landscape,...

2026-06-10 | MTBLS10469 | MetaboLights
MetabolomicsHistone H3K4me3 Demethylase RBP2 Transcriptionally Activates PPARγ to Drive Lipid Metabolic Reprogramming in Gastric Carcinoma

This work investigates epigenetic driven lipid metabolic reprogramming in gastric carcinoma. We characterize that histone H3K4me3 demethylase RBP2 transcriptionally activates PPARgama by binding to its promoter region,thereby promoting lipogenic gene expression and intracellular lipid accumulatio...

2026-08-14 | MTBLS15324 | MetaboLights
GenomicsH3K4me3 modification profiling of Huntingtons disease and control human post-mortem prefrontal cortex brain samples
Huntington’s disease (HD) is an autosomal-dominant neurodegenerative disorder resulting from expansion in the number of CAG repeats in the coding region of exon 1 of the Huntingtin (HTT) gene. One of the most widely studied chromatin modifications is trimethylated lysine 4 of histone 3 (H3K4me3). ...
ORGANISM(S): Homo sapiens 
2015-12-14 | E-GEOD-68952 | biostudies-arrayexpress
GenomicsLID ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster
LID is a histone demethylase acting on H3K4me3, a mark related to transcription and found near the transcription start sites (TSS) of the genes. We analyzed where LID is localized and the effects of LID downregulation in the distribution of H3K4me3. Analysis of LID-binding sites in wild type, and of...
ORGANISM(S): Drosophila melanogaster 
2012-08-30 | E-GEOD-27078 | biostudies-arrayexpress
GenomicsMapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts
Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantl...
ORGANISM(S): Oreochromis niloticus 
2015-07-07 | E-GEOD-62791 | biostudies-arrayexpress
GenomicsA Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence [ChIP-seq]
The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 mark...
ORGANISM(S): Arabidopsis thaliana 
2015-04-11 | E-GEOD-67776 | biostudies-arrayexpress
TranscriptomicsReplication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast
Histone modifications affect DNA-templated processes ranging from transcription to genomic replication. In this study, we examine the cell cycle dynamics of the trimethylated form of histone H3 lysine 4 (H3K4me3), a mark of active chromatin that is viewed as â??long-livedâ?? [1], and that is involve...
ORGANISM(S): Saccharomyces cerevisiae 
2010-06-24 | E-GEOD-14565 | biostudies-arrayexpress
GenomicsBivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline in Vivo
We developed a ChIP protocol for the analysis of histone marks using less than 10,000 cells per IP, and used it to investigate the chromatin state of E11.5 mouse primordial germ cells (PGCs). A genome-wide ChIP-Seq analysis of E11.5 PGCs revealed a distribution of H3K4me3/H3K27me3 bivalent domains h...
ORGANISM(S): Mus musculus 
2013-05-30 | E-GEOD-46396 | biostudies-arrayexpress
GenomicsThe Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq KYSE150 cell line)
We have mapped binding sites for the histone demethylase, JMJD2C/KDM4C/GASC1, and the effect of JMJD2C depletion on H3K9me3 and H3K36me3 distributions in KYSE150 cells. The human esophageal carcinoma cell line, KYSE150, contains an amplification of the JMJD2C locus. ChIP-seq was performed using chr...
ORGANISM(S): Homo sapiens 
2014-01-09 | E-GEOD-53938 | biostudies-arrayexpress
GenomicsCfp1 is required for gene expression dependent H3K4me3 and H3K9 acetylation in embryonic stem cells (ChIP-Seq)
Trimethylation of histone H3 lysine 4 (H3K4me3) accumulates at promoters in a gene activity dependant manner. The Set1 complex is responsible for most H3K4me3 in somatic cells and contains the conserved subunit Cfp1, which is implicated in targeting the Set1 complex to CpG islands in mammals. In mou...
ORGANISM(S): Mus musculus 
2014-08-20 | E-GEOD-53490 | biostudies-arrayexpress
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