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Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos [ChIP-Seq 2]

ABSTRACT: To further investigate the relationship between abnormal accumulation of H3K4me3 modification and abnormal embryo development. We injected Kdm5b siRNA, which is an H3K4me3 eraser, at the zygote (PN3-PN4) stage of NM embryos and then examined the H3K4me3 modification of extraembryonic ectoderm at E7.5.

ORGANISM(S): Mus musculus

PROVIDER: GSE197920 | GEO | 2022/05/26

REPOSITORIES: GEO

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Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos [RNA-Seq 3]

Project description:To further investigate the relationship between abnormal accumulation of H3K4me3 modification and abnormal embryo development. We injected Kdm5b siRNA, which is an H3K4me3 eraser, at the zygote (PN3-PN4) stage of NM embryos and then examined the transcriptome of extraembryonic ectoderm at E7.5.

2022-05-26 | GSE197914 | GEO

Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (ChIP-Seq)

Project description:Assisted reproductive technology (ART), especially in vitro fertilization (IVF) and embryo transfer have been widely applied in the treatment of human infertility. However, the accumulating evidences indicate that IVF is associated with low pregnancy rate, placental defect and the metabolic diseases in offspring. Here, we identify ectopic histone H3K4me3 in extraembryonic ectoderm (ExE) as an important reason for embryo implantation failure and extra-embryonic development abnormalities of IVF embryos. IVF manipulation notably disrupt extra-embryonic tissue-specific gene expression, 334 epiblast (Epi)-specific genes and 24 Epi-specific transcription factors were abnormally expressed in ExE of IVF embryos at embryonic day 7.5 (E7.5). Combined histone modification analysis reveal that ectopic H3K4me3 modification at the Epi-active promoter resulted in increased expression of these genes in ExE of IVF embryos at E7.5. By konckdown the expression of H3K4me3 recruited regulator Kmt2e, which highly expressed in IVF embryos, can improve the development of IVF embryo and reduce the abnormal gene expression in ExE. Therefore, our research identifies the abnormal H3K4me3 modification occupied in extra-embryonic tissue may be an important reason for implantation failure and abnormal placental development of IVF embryo.

2022-05-26 | GSE168269 | GEO

Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (RNA-Seq 2)

2022-05-26 | GSE168273 | GEO

Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (RNA-Seq 1)

2022-05-26 | GSE168272 | GEO

Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos

Project description:Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos

| PRJNA706709 | ENA

Extended self-renewal and accelerated reprogramming in the absence of Kdm5b [ChIP-Seq]

Project description:ES cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in iPS cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation, and presents a barrier to the reprogramming process. Depletion of Kdm5b leads to an extension in the self-renewal of ES cells in the absence of LIF. Transcriptome analysis revealed the persistent expression of pluripotency-genes and underexpression of developmental genes during differentiation in the absence of Kdm5b, suggesting that KDM5B plays a key role in cellular fate changes. We also observed accelerated reprogramming of differentiated cells in the absence of Kdm5b, demonstrating that KDM5B is a barrier to the reprogramming process. Expression analysis revealed that mesenchymal master regulators associated with epithelial-to-mesenchymal transition (EMT) are downregulated during reprogramming in the absence of Kdm5b. Moreover, global analysis of H3K4me3/2 revealed that enhancers of fibroblast genes are rapidly deactivated in the absence of Kdm5b, and genes associated with EMT lose H3K4me3/2 during the early reprogramming process. These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process. ChIP-Seq for H3K4me3 and H3K4me2 in murine shLuc and shKdm5b 4TF-MEFs (tetO-Pou5f1,-Sox2,-Klf4,-c-Myc) at 48h.

2013-10-14 | E-GEOD-47123 | biostudies-arrayexpress

Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos

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

2022-05-25 | GSE168274 | GEO

Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing

Project description:Positioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how post-translational modification of histones such as activating trimethylated histone 3 lysine 4 (H3K4me3), or histone demethylases including the H3K4 demethylase, KDM5B, impacts nucleosome positioning around transcriptional start sites (TSS) of active genes is poorly understood. Here, we report that KDM5B is a critical regulator of nucleosome positioning in embryonic stem (ES) cells. Micrococcal nuclease sequencing (MNase-Seq) revealed increased enrichment of nucleosomes around TSS regions and DNase I hypersensitive sites in KDM5B-depleted ES cells. Moreover, depletion of KDM5B resulted in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner. Dysregulated nucleosome phasing was also evident in KDM5B-depleted ES cells, including asynchronous nucleosome spacing surrounding TSS regions, where nucleosome variance was positively correlated with the degree of asynchronous phasing. The redistribution of nucleosomes around TSS regions in KDM5B-depleted ES cells is correlated with dysregulated gene expression, and altered H3K4me3 and RNA polymerase II occupancy. In addition, we found that DNA shape features varied significantly at regions with shifted nucleosomes. Altogether, our data support a role for KDM5B in regulating nucleosome positioning in ES cells.

2019-04-23 | GSE123249 | GEO

Extended self-renewal and accelerated reprogramming in the absence of Kdm5b [RNA-Seq]

Project description:ES cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in iPS cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation, and presents a barrier to the reprogramming process. Depletion of Kdm5b leads to an extension in the self-renewal of ES cells in the absence of LIF. Transcriptome analysis revealed the persistent expression of pluripotency-genes and underexpression of developmental genes during differentiation in the absence of Kdm5b, suggesting that KDM5B plays a key role in cellular fate changes. We also observed accelerated reprogramming of differentiated cells in the absence of Kdm5b, demonstrating that KDM5B is a barrier to the reprogramming process. Expression analysis revealed that mesenchymal master regulators associated with epithelial-to-mesenchymal transition (EMT) are downregulated during reprogramming in the absence of Kdm5b. Moreover, global analysis of H3K4me3/2 revealed that enhancers of fibroblast genes are rapidly deactivated in the absence of Kdm5b, and genes associated with EMT lose H3K4me3/2 during the early reprogramming process. These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process. RNA-Seq of undifferentiated and embryoid body (EB) differentiated murine shLuc and shKdm5b ES cells

2013-10-14 | E-GEOD-47124 | biostudies-arrayexpress

Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (ChIP-Seq)

Project description:Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (ChIP-Seq)

| PRJNA706714 | ENA

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