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H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [RNA-seq]

ABSTRACT: To investigate the differential expression pattern between wild type mESC cells and PRC2-deficient cells. We established Eed-KO and Suz12-KO cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of these different cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE217248 | GEO | 2023/04/05

REPOSITORIES: GEO

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H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [ChIP-seq]

Project description:Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for LSD1 as well as histone modifications H3K4me1, H3K4me3 and H3K27me3 in WT OG2 mESC cells and its KO derivatives (Eed-KO and Suz12-KO ).

2023-04-05 | GSE217247 | GEO

H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development.

Project description:BackgroundBivalent genes, of which promoters are marked by both H3K4me3 (trimethylation of histone H3 on lysine 4) and H3K27me3 (trimethylation of histone H3 on lysine 27), play critical roles in development and tumorigenesis. Monomethylation on lysine 4 of histone H3 (H3K4me1) is commonly associated with enhancers, but H3K4me1 is also present at promoter regions as an active bimodal or a repressed unimodal pattern. Whether the co-occurrence of H3K4me1 and bivalent marks at promoters plays regulatory role in development is largely unknown.ResultsWe report that in the process of lineage differentiation, bivalent promoters undergo H3K27me3-H3K4me1 transition, the loss of H3K27me3 accompanies by bimodal pattern loss or unimodal pattern enrichment of H3K4me1. More importantly, this transition regulates tissue-specific gene expression to orchestrate the development. Furthermore, knockout of Eed (Embryonic Ectoderm Development) or Suz12 (Suppressor of Zeste 12) in mESCs (mouse embryonic stem cells), the core components of Polycomb repressive complex 2 (PRC2) which catalyzes H3K27 trimethylation, generates an artificial H3K27me3-H3K4me1 transition at partial bivalent promoters, which leads to up-regulation of meso-endoderm related genes and down-regulation of ectoderm related genes, thus could explain the observed neural ectoderm differentiation failure upon retinoic acid (RA) induction. Finally, we find that lysine-specific demethylase 1 (LSD1) interacts with PRC2 and contributes to the H3K27me3-H3K4me1 transition in mESCs.ConclusionsThese findings suggest that H3K27me3-H3K4me1 transition plays a key role in lineage differentiation by regulating the expression of tissue specific genes, and H3K4me1 pattern in bivalent promoters could be modulated by LSD1 via interacting with PRC2.

| S-EPMC10061859 | biostudies-literature

H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-04-05 | GSE217249 | GEO

H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development.

Project description:H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development.

| PRJNA898276 | ENA

H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [RNA-seq]

Project description:H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [RNA-seq]

| PRJNA898283 | ENA

H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [ChIP-seq]

Project description:H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [ChIP-seq]

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Identification of a novel role of MTF2 in the regulation of H3K27me3 by PRC2 (RNA-Seq)

Project description:We sequenced mRNA from F9 cells after knockdown of EZH2, SUZ12 and EED by shRNA. EZH2, SUZ12 and EED are the core componnets of PRC2 which repress its target genes by H3K27me3.

2018-02-27 | GSE111145 | GEO

H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs [RNA-Seq]

Project description:Suz12(Bgal/Bgal) ESCs express a truncated form of Suz12 fused to Beta-galactosidase. These cells maintain a reduced level of H3K27me3 despite this mutation to a core component of PRC2, unlike Eed-/- ESCs whose H3K27me3 is ablated. RNA-seq was performed in wild type and Suz12(Bgal/Bgal) ESCs, here used to demonstrate the coverage of the Suz12 gene in mRNA reads.

2013-07-22 | E-GEOD-47484 | biostudies-arrayexpress

H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs [RNA-Seq]

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H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs [ChIP-Seq]

2013-07-22 | GSE47483 | GEO