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KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE111848 | GEO | 2018/06/14

REPOSITORIES: GEO

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KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation.

Project description:Trophoblast stem (TS) cells derived from the trophectoderm (TE) of mammalian embryos have the ability to self-renew indefinitely or differentiate into fetal lineages of the placenta. Epigenetic control of gene expression plays an instrumental role in dictating the fate of TS cell self-renewal and differentiation. However, the roles of histone demethylases and activating histone modifications such as methylation of histone 3 lysine 4 (H3K4me3/me2) in regulating TS cell expression programs, and in priming the epigenetic landscape for trophoblast differentiation, are largely unknown. Here, we demonstrate that the H3K4 demethylase, KDM5B, regulates the H3K4 methylome and expression landscapes of TS cells. Depletion of KDM5B resulted in downregulation of TS cell self-renewal genes and upregulation of trophoblast-lineage genes, which was accompanied by altered H3K4 methylation. Moreover, we found that KDM5B resets the H3K4 methylation landscape during differentiation in the absence of the external self-renewal signal, FGF4, by removing H3K4 methylation from promoters of self-renewal genes, and of genes whose expression is enriched in TS cells. Altogether, our data indicate an epigenetic role for KDM5B in regulating H3K4 methylation in TS cells and during trophoblast differentiation.

| S-EPMC5992522 | biostudies-literature

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [RNA-seq]

2018-06-14 | GSE111847 | GEO

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [ChIP-seq]

2018-06-14 | GSE111846 | GEO

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation

Project description:KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation

| PRJNA438346 | ENA

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation.

Project description:BackgroundPluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function.ResultsHere, we show that KDM5B, which demethylates lysine 4 of histone H3, co-localizes with H3K4me3 near promoters and enhancers of active genes in ES cells; its depletion leads to spreading of H3K4 methylation into gene bodies and enhancer shores, indicating that KDM5B functions to focus H3K4 methylation at promoters and enhancers. Spreading of H3K4 methylation to gene bodies and enhancer shores is linked to defects in gene expression programs and enhancer activity, respectively, during self-renewal and differentiation of KDM5B-depleted ES cells. KDM5B critically regulates H3K4 methylation at bivalent genes during differentiation in the absence of LIF or Oct4. We also show that KDM5B and LSD1, another H3K4 demethylase, co-regulate H3K4 methylation at active promoters but they retain distinct roles in demethylating gene body regions and bivalent genes.ConclusionsOur results provide global and functional insight into the role of KDM5B in regulating H3K4 methylation marks near promoters, gene bodies, and enhancers in ES cells and during differentiation.

| S-EPMC4053761 | biostudies-literature

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [RNA-seq]

Project description:KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [RNA-seq]

| PRJNA438403 | ENA

KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [ChIP-seq]

Project description:KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation [ChIP-seq]

| PRJNA438402 | ENA

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-01-27 | E-GEOD-53093 | biostudies-arrayexpress

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation

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

2014-01-27 | GSE53093 | GEO

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [RNA-Seq]

Project description:Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. Here, we show that KDM5B, which demethylates lysine 4 of histone H3, co-localizes with H3K4me3 near promoters and enhancers of active genes in ES cells; its depletion leads to spreading of H3K4 methylation into gene bodies and enhancer shores, indicating that KDM5B functions to focus H3K4 methylation at promoters and enhancers. Spreading of H3K4 methylation to gene bodies and enhancer shores is linked to defects in gene expression programs and enhancer activity, respectively, during self-renewal and differentiation of KDM5B-depleted ES cells. KDM5B critically regulates H3K4 methylation at bivalent genes during differentiation in the absence of LIF or Oct4. We also show that KDM5B and LSD1, another H3K4 demethylase, co-regulate H3K4 methylation at active promoters but they retain distinct roles in demethylating gene body regions and bivalent genes. Our results provide global and functional insight into the role of KDM5B in regulating H3K4 methylation marks near promoters, gene bodies, and enhancers in ES cells and during differentiation. RNA-Seq of murine shLuc and shKdm5b ES cells differentiated for 72h in the absence of LIF.

2014-01-27 | E-GEOD-53090 | biostudies-arrayexpress

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