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An enhancer cluster promotes NPCs formation from ESCs through maintaining HoxB activation by long-range chromatin interaction

ABSTRACT: An enhancer cluster promotes NPCs formation from ESCs through maintaining HoxB activation by long-range chromatin interaction

PROVIDER: PRJNA668717 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12809334_1.fastq.gz	Fastqsanger.gz
	SRR12809334_2.fastq.gz	Fastqsanger.gz
	SRR12809335_1.fastq.gz	Fastqsanger.gz
	SRR12809335_2.fastq.gz	Fastqsanger.gz
	SRR12809336_1.fastq.gz	Fastqsanger.gz

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An enhancer cluster promotes NPCs formation from ESCs through maintaining HoxB activation by long-range chromatin interaction

Project description:Homeobox B cluster genes (HoxB) are important marker genes for neural progenitor cells (NPCs) formation from embryonic stem cells (ESCs). However, mechanisms of HoxB activation in NPCs remain largely unknown. Here, we find an enhancer cluster (EnC) interacting with the HoxB locus by PLAC-seq analysis. CRISPR/Cas9-mediated EnC deletion significantly inhibited HoxB expression, indicating that the EnC is required for HoxB activation in NPCs. Transcriptome analysis revealed that differentiation-related master control genes and NPCs formation-related signaling pathways were significantly inhibited suggesting that the EnC is essential for NPCs formation. In summary, our results reveal a new mechanism about HoxB activation depending on EnC is crucial for NPCs formation.

2020-10-13 | GSE159378 | GEO

Two enhancers synergistically regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure

Project description:Homeobox B cluster (HoxB) genes play important roles in RA-induced early ESCs differentiation. In this study, we identified two enhancers synergistically regulate HoxB genes expressions through 3D chromatin structure and thus regulate RA-induced early ESCs differentiation. 4C data showed interactions between HoxB genes and the two enhancers. CRISPR/Cas9-mediated individual or compound deletion of the two enhancers significantly inhibits HoxB genes expressions while transcriptome analysis revealed that RA induced early ESCs differentiation was blocked in the enhancer KO cells. Our study suggests new mechanism by which two enhancers regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure.

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ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs

Project description:We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers. Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage. Examination of transcription factor binding in ESCs, NPCs, and differentiating ESCs by ChIP-Seq.

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ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs

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Expression profiling of mouse embryonic stem cells (ESCs) (cell line V6.5, 129SvJae/C57B6 F1 background), and mouse ESC-derived Neural Precursor Cells (NPCs)

Project description:ESCs and NPCs are two setm cell types which rely on expression of the transcription factor Sox2. We profilled gene expression in ESCs and NPCs to correlate genome-wide Sox2 ChIP-Seq data in these cells with expression of putative targets Three biological replicates each of ESCs and NPCs were prepared and assays using Affymetrix Gene Expression Arrays

2013-02-20 | E-GEOD-38850 | biostudies-arrayexpress

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Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation

Project description:Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation

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The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia

Project description:In this work we dissect the functional role of the HOXB-AS3 long non coding RNA in patients with NPM1-mutated (NPM1mut) acute myeloid leukemia (AML). We show that HOXB-AS3 regulates the proliferative capacity of NPM1mut AML blasts in vitro and in vivo. HOXB-AS3 was found to interact with the ErbB3-binding protein 1 (EBP1) and guide EBP1 to the ribosomal DNA locus. Via this mechanism HOXB-AS3 regulates ribosomal RNA transcription and de novo protein synthesis. We propose that in the context of NPM1 mutations, HOXB-AS3 overexpression acts as a compensatory mechanism, which allows adequate protein production in leukemic blasts.

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Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation

Project description:Inhibitors of MEK1/2 and Gsk3b, known as '2i' culture conditions, enhance the derivation of embryonic stem cells (ESCs) and promote ground-state pluripotency in rodents 1,2. Here we show that the derivation of female mouse ESCs in the presence of 2i (2i-ESCs) results in a widespread loss of DNA methylation including a massive erasure of genomic imprints. Despite this global loss of DNA methylation, the early-passage 2i-ESCs efficiently differentiate into somatic cells and this process requires genome-wide de novo DNA methylation. However, the majority of imprinting control regions (ICRs) remain unmethylated in the 2i-ESC-derived differentiated cells. Consistently, 2i-ESCs exhibit impairment of autonomous embryonic and placental development by tetraploid embryo complementation and nuclear transplantation. We identified the derivation conditions of female ESCs that display 2i-ESC-like transcriptional signatures while preserving gamete-derived DNA methylation and autonomous developmental potential. Upon prolonged culture, however, female ESCs exhibit ICR demethylation, regardless of culture conditions. Our results provide insights into derivation of female ESCs reminiscent of ICM of preimplantation embryos. S-ESCs are ESCs established under serum-containing medium. 2i_S_ESCs are ESCs established in 2i-containing medium, followed by maintenance in serum-containing medium.

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