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Opposing Role of Dpf2 and Eed on Differentiation of Mouse Embryonic Stem Cells via Regulating Tbx3 (RNA-seq)

ABSTRACT: RNA-seq experiments of wild-type E14 cells and Dpf2 knockout cells (OHT treated)

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Xi Chen

PROVIDER: E-MTAB-6166 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Opposing Role of Dpf2 and Eed on Differentiation of Mouse Embryonic Stem Cells via Regulating Tbx3 (4C)

Project description:4C experiments of wild-type and Dpf2 -/- cells to investigate the effect of Dpf2 on the chromatin contacts of Tbx3 locus.

2018-11-30 | E-MTAB-6197 | biostudies-arrayexpress

Opposing Role of Dpf2 and Eed on Differentiation of Mouse Embryonic Stem Cells via Regulating Tbx3 (ChIP-seq)

Project description:ChIP-seq experiments of 3xFlag-Dpf2, Oct4, Sox2 and several histone marks were performed in wild-type and Dpf2 -/- cells to investigate the effect of Dpf2 on the binding of those factors.

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The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation.

Project description:BAF complexes are composed of different subunits with varying functional and developmental roles, although many subunits have not been examined in depth. Here we show that the Baf45 subunit Dpf2 maintains pluripotency and ESC differentiation potential. Dpf2 co-occupies enhancers with Oct4, Sox2, p300, and the BAF subunit Brg1, and deleting Dpf2 perturbs ESC self-renewal, induces repression of Tbx3, and impairs mesendodermal differentiation without dramatically altering Brg1 localization. Mesendodermal differentiation can be rescued by restoring Tbx3 expression, whose distal enhancer is positively regulated by Dpf2-dependent H3K27ac maintenance and recruitment of pluripotency TFs and Brg1. In contrast, the PRC2 subunit Eed binds an intragenic Tbx3 enhancer to oppose Dpf2-dependent Tbx3 expression and mesendodermal differentiation. The PRC2 subunit Ezh2 likewise opposes Dpf2-dependent differentiation through a distinct mechanism involving Nanog repression. Together, these findings delineate distinct mechanistic roles for specific BAF and PRC2 subunits during ESC differentiation.

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Opposing Role of Dpf2 and Eed on Differentiation of Mouse Embryonic Stem Cells via Regulating Tbx3 (4C)

Project description:Opposing Role of Dpf2 and Eed on Differentiation of Mouse Embryonic Stem Cells via Regulating Tbx3 (4C)

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Opposing Role of Dpf2 and Eed on Differentiation of Mouse Embryonic Stem Cells via Regulating Tbx3 (RNA-seq)

Project description:Opposing Role of Dpf2 and Eed on Differentiation of Mouse Embryonic Stem Cells via Regulating Tbx3 (RNA-seq)

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Dpf2 interactome in mouse embryonic stem cells

Project description:Dpf2 is a subunit of the BAF/pBAF chromatin remodelling complex. We have used cross-linking affinity purification-mass spectrometry to explore Dpf2 protein interactions in mouse embryonic stem cells.

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Simulated microgravity regulates the self-renewal and pluripotency of mouse and human embryonic stem cells - RNA-seq

Project description:Human exploration of outer space will inevitably require human reproduction and development in the space environment. Embryonic stem cells (ESCs) are widely employed to study mammalian development and reproduction for their characteristics of indefinite self-renewal and pluripotency. Due to the lack of experimental opportunities and related techniques, studies of the effects of microgravity on the self-renewal and differentiation of ESCs are mostly descriptive, with in-depth mechanistic studies remaining scarce. Here we show in both mouse and human ESCs that simulated microgravity (SMG)-induced stress regulates the self-renewal and pluripotency in a conserved mechanism. Specifically, SMG upregulates the expression of heat shock protein (HSP) and/or HSF1 genes, thereby increasing the expression of core pluripotency factors and the activity of the Wnt pathway. In mESCs, the upregulation of Hsps and Hsf1 genes by SMG increased the activity of the LIF/STAT3 pathway. The upregulation of Tbx3 by increased activity of the Wnt and LIF/STAT3 pathways promotes the differentiation of both mouse and human ESCs to mesendoderm under the SMG environment. Finally, the ATAC-seq and ChIP-seq analysis in this study reveal a minor effect of SMG on the global chromatin accessibility and the overall patterns of the tested histone modifications in mESCs.

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ChIP-Seq to investigate the opposing role of Dpf2 and Eed on differentiation of Mouse Embryonic Stem Cells via regulating Tbx3

Project description:ChIP-Seq to investigate the opposing role of Dpf2 and Eed on differentiation of Mouse Embryonic Stem Cells via regulating Tbx3

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Genome-wide maps of DPF2 and H3K14 modifications in K562 cells

Project description:we report DPF2 and H3K14 modifications in K562 cells

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DPF2 reads histone lactylation to drive transcription and tumorigenesis [CUT&TAG]

Project description:Lysine lactylation (Kla) is a new type of histone mark implicated in the regulation of various functional processes such as transcription. However, how this histone mark acts in cancers remains unexplored due in part to a lack of knowledge about its reader proteins. Here, we observe that cervical cancer (CC) cells undergo metabolic reprogram by which lactate accumulation and thereby boost histone lactylation, particularly H3K14la. Utilizing a multivalent photoaffinity probe in combination with quantitative proteomics approach, we identify DPF2 as a candidate target of H3K14la. Biochemical studies as well as CUT&Tag analysis reveal that DPF2 is capable of binding to H3K14la, and co-localizes with it on promoters of oncogenic genes. Notably, disrupting the association between DPF2 and histone lactylation through structure-guided mutation blunts those cancer-related gene expression along with cell survival. Together, our findings reveal DPF2 as a bona fide H3K14la effector that couples histone lactylation to gene transcription and cell survival, offering insight into how histone Kla engages in transcription and tumorigenesis.

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