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Histone H3 lysine 9 tri-methylation is associated with pterygium

ABSTRACT: Histone H3 lysine 9 tri-methylation is associated with pterygium

PROVIDER: PRJNA1137234 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29873947_1.fastq.gz	Fastqsanger.gz
	SRR29873947_2.fastq.gz	Fastqsanger.gz
	SRR29873948_1.fastq.gz	Fastqsanger.gz
	SRR29873948_2.fastq.gz	Fastqsanger.gz
	SRR29873949_1.fastq.gz	Fastqsanger.gz

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Histone H3 lysine 9 tri-methylation is associated with pterygium

Project description:Pterygium, abnormal growths of conjunctival tissue onto the cornea, are common ocular surface conditions with a high risk of recurrence after surgery and potential ophthalmic complications. The exact cause of pterygium remains unclear, and the triggers are still unknown. In this study, we investigate the epigenetic profiles of patients with pterygium, focusing on histone H3 lysine 4 (H3K4) and lysine 9 (H3K9) trimethylation (me3). While H3K4me3 levels showed no significant genome-wide change, they were significantly altered in genes related to development and ocular diseases. Conversely, H3K9me3 levels were markedly elevated genome-wide, particularly at the promoters of 82 genes involved in developmental pathways. Furthermore, we identify six genes, ANK2, AOAH, CBLN2, CDH8, CNTNAP4, and DPP6, with decreased gene expression correlated with substantially increased H3K9me3, suggesting their potential as biomarkers for pterygium. This study represents the first report linking histone modification to pterygium progression, providing valuable insights into therapeutic strategies and potential drug targets.

2025-01-19 | GSE272511 | GEO

Time makes histone H3 modifications drift

Project description:To disclose the epigenetic drift of time passing, we determined the genome-wide distributions of mono- and tri-methylated lysine 4 and acetylated and tri-methylated lysine 27 of histone H3 in the livers of healthy 3, 6 and 12 months old C57BL/6 mice. The comparison of different age profiles of histone H3 marks revealed global redistribution of histone H3 modifications with time, in particular in intergenic regions and near transcription start sites, as well as altered correlation between the profiles of different histone modifications. Moreover, feeding mice with caloric restriction diet, a treatment known to retard aging, preserved younger state of histone H3 in these genomic regions.

2022-07-13 | GSE179090 | GEO

CpG islands recruit a histone H3 lysine 36 demethylase

Project description:This SuperSeries is composed of the following subset Series: GSE18588: CpG islands recruit a histone H3 lysine 36 demethylase [Illumina sequencing data] GSE21201: CpG islands recruit a histone H3 lysine 36 demethylase [Agilent data] Refer to individual Series

2010-04-26 | E-GEOD-21202 | biostudies-arrayexpress

NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming

Project description:This SuperSeries is composed of the following subset Series: GSE29146: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [ChIP] GSE29147: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [RNAi] GSE29148: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [TKO] GSE29150: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [Transduction] Refer to individual Series

2011-11-29 | E-GEOD-29305 | biostudies-arrayexpress

Localization of histone H3 and histone H3 lysine 4 trimethylation at the start of pre-meiotic S phase

Project description:ChIP-on-chip analysis of histone H3 and histone H3 lysine 4 trimethylation in cells induced to undergo synchronous meiosis after growth in nitrogen-rich conditions or after nitrogen depletion. Comparison of H3 and H3k4Me3 in diploid pat1-114 cells grown in -N and +N conditions.

2014-02-20 | E-GEOD-53878 | biostudies-arrayexpress

A critical density of histone H3 lysine 9 tri-methylation is required for propagation of heterochromatin and epigenetic inheritance

Project description:Occupancy profiling of myc-tagged Raf1 protein in fission yeast. Occupancy profiling of lysine 9 dimethylated and trimethylated histone H3 in fission yeast.

2021-06-09 | GSE162701 | GEO

Histone H3 lysine 27 trimethylation of miRNA genes in HMEC and HMF

Project description:Normal cell type specific histone H3 lysine 27 trimethylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 lysine 27 trimethylation affect miRNA expression. Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-histone H3 trimethylated at lysine 27 (07-449, Millipore).

2011-04-05 | E-GEOD-28376 | biostudies-arrayexpress

Histone H3 lysine 4 trimethylation of miRNA genes in HMEC and HMF

Project description:Normal cell type specific histone H3 lysine 4 trimethylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 lysine 4 trimethylation affect miRNA expression. Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-histone H3 trimethylated at lysine 4 (05-745, Upstate).

2011-04-05 | E-GEOD-28377 | biostudies-arrayexpress

Histone H3 lysine 9 dimethylation of miRNA genes in HMEC and HMF

Project description:Normal cell type specific histone H3 lysine 9 dimethylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 lysine 9 dimethylation affect miRNA expression. Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-histone H3 dimethylated at lysine 9 (CS200587, Millipore).

2011-04-05 | E-GEOD-28378 | biostudies-arrayexpress

Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids

Project description:In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 from me0 through histone H2B mono-ubiquitin interaction. The early-branched kinetoplastid Trypanosoma brucei harbors the essential H3K76 di-methyltransferase DOT1A and the non-essential DOT1B H3K76 tri-methyltransferase, which methylate their substrates without H2B mono-ubiquitination. It is not known how these enzymes efficiently maintain H3K76me3 without ubiquitin interaction in vivo. Here we discovered distinct methylation kinetics of DOT1A and DOT1B in vitro and identified kinetoplastid-specific key residues by structural analysis of DOT1A. DOT1A contains a unique N-terminal ?-hairpin domain and a conserved C-terminal methyltransferase core domain that exhibits significant deviations in the methyltransferase motifs IV, VI, and X. The motif X sequence VYGE is substituted to CAKS in a non-conserved, flexible active-site loop, implying a distinct mechanism for substrate H3K76 recognition. Substitution of a basic to an acidic residue within the canonical motif VI (Gx6K) at the putative DOT1A-nucleosome interface is essential for DOT1A-nucleosome interaction, which would stabilize the enzyme-substrate complex without ubiquitin interactions. Mass spectrometry-based kinetic data demonstrate that DOT1A favors H3K76me0, while DOT1B favors the DOT1A products H3K76me1 and me2. These substrate preferences are determined by Ser and Ala residues within motif IV of DOT1A and DOT1B, respectively. We show in vitro that the distinct substrate preferences enable DOT1A and DOT1B to catalyze H3K76 tri-methylation eight times faster than DOT1B alone, suggesting that efficient ubiquitin-independent H3K76 tri-methylation can be achieved non-processively through the cooperative action of two DOT1 enzymes in vivo.

2022-11-09 | MSV000090680 | MassIVE

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