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ATAC-seq analyses with wild-type and PML KO mESCs

ABSTRACT: ATAC-seq analyses with wild-type and PML KO mESCs

PROVIDER: PRJNA559287 | ENA |

REPOSITORIES: ENA

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ATAC-seq analyses with wild-type and PML KO mESCs

Project description:Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate functional roles of PML bodies in chromatin organization, we conducted ATAC-seq with wild-type and PML KO mESCs.

2019-08-14 | GSE135561 | GEO

RNA-seq analyses of wild-type and PML KO mESCs

Project description:Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin. To address roles of PML bodies in transcriptional regulation, we performed RNA-seq analyses with wild-type and PMK knockout mESCs

2019-08-14 | GSE135557 | GEO

RNA-seq analyses of wild-type and PML KO mESCs

Project description:RNA-seq analyses of wild-type and PML KO mESCs

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ChIP-seq analysis of wild-type and PML KO mESCs

Project description:Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate roles of PML bodies in transcriptional regulation, we conducted ChIP-seq analysis for histone modifications, including H3K4me3, H3K27ac, H3K27me3, and H3K9ac with wild-type and PML knockout mESCs.

2019-08-14 | GSE135562 | GEO

ChIP-seq analysis of wild-type and PML KO mESCs

Project description:ChIP-seq analysis of wild-type and PML KO mESCs

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Recruitment of TRIM33 to cell-context specific PML nuclear bodies regulates Nodal signaling in mESCs

Project description:TRIM33 is a chromatin reader required for mesendoderm differentiation upon activation of Nodal signaling. But, its role in mESCs is still elusive. Here, we found that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML NBs) specifically in mESCs to mediate Nodal signaling-directed transcription of Lefty1/2. We showed that TRIM33 puncta formation in mESCs depends on PML and specific assembly of PML NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs. In addition, both PML and mESCs-specific PML NBs are required for TRIM33 recruitment at Lefty1/2 loci. Remarkably, PML NBs directly associate with the Lefty1/2 loci in mESCs. Finally, a TurboID proximity labeling experiment confirmed that TRIM33 is highly enriched in the mESCs-specific PML NBs. Thus, our study provides the mechanistic insight about TRIM33 condensate in regulating Nodal signaling-directed transcription in mESCs, it also reveals that PML NBs recruit distinct sets of client proteins in cell context dependent manner.

2022-12-08 | GSE199738 | GEO

Role of PML in repression of transposable elements and in embryonic stem cell fate

Project description:Microarrays transcriptomic data analyses from 3 Pml-/- and 3 Pml+/+ mESCs samples

2022-02-01 | E-MTAB-10151 | biostudies-arrayexpress

Gene expression profiling of Pml wt and Pml KO mice liver after fasted 6h

Project description:The Pml gene is essential to the formation of PML nuclear bodies, domains which have been associated with various functions such as apoptosis/senescence, DNA repair and cell proliferation( Lallemand-Breitenbach 2010). PML-NBs formation is regulated by cellular stress including oxidative stress(Jeanne 2010, de The 2012). To investigate the role of PML in ROS response in vivo, we analyse the expression difference betweem Pml wt and Pml KO under fasted condition, which easily up-regulate ROS in BALB/cByJ background

2017-09-22 | GSE100615 | GEO

ATAC-seq of mESCs differentiation into neurons

Project description:Mouse WT129 ESCs were differentiated into glutamatergic neurons and samples were collected at days 0 (mESCs), 4 (embryoid bodies), 8 (neuronal precursors) and 12 (neurons). ATAC-seq experiment in 4 biological replicates was performed at 4 indicated above time points to profile chromatin structure changes during differentiation.

2020-05-20 | E-MTAB-8194 | biostudies-arrayexpress

ALaP-seq and RNA-seq analyses of paraquat treated mESCs

Project description:To address the roles of PML bodies in transcription under stress condition, we performed ALaP-seq and RNA-seq with paraquat treated mESCs.

2020-01-10 | GSE143361 | GEO

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