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Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [RNA-seq]

ABSTRACT: Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [RNA-seq]

PROVIDER: PRJNA573658 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10163457_1.fastq.gz	Fastqsanger.gz
	SRR10163457_2.fastq.gz	Fastqsanger.gz
	SRR10163458_1.fastq.gz	Fastqsanger.gz
	SRR10163458_2.fastq.gz	Fastqsanger.gz
	SRR10163459_1.fastq.gz	Fastqsanger.gz

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Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [RNA-seq]

Project description:Chromatin modifiers affect the spatiotemporal expression of gene expression programs that underlie organismal development. The Polycomb repressive complex 2 (PRC2) has emerged as a crucial player in executing neurodevelopmental programs. Here we show that the nucleic acid–binding protein Ybx1 interacts with PRC2 in human and mouse neural progenitor cells (NPCs). During early neural development in vivo, Ybx1 is required for forebrain specification and modulates mid/hindbrain growth. In NPCs, Ybx1 controls the self-renewal and neuronal differentiation. Mechanistically, Ybx1 binds PRC2 gene targets, reduces the levels of PRC2-mediated H3K27me3, and promotes the expression of genes in forebrain specification, cell proliferation, or neuronal differentiation. In Ybx1-knockout NPCs, H3K27me3 reduction by PRC2 enzymatic inhibitor or genetic depletion partially rescues the control of gene expression, self-renewal, and neuronal differentiation. Our findings suggest that Ybx1 modulates H3K27me3 by PRC2 to regulate spatiotemporal gene expression in embryonic neural development and uncover a crucial epigenetic mechanism balancing forebrain–hindbrain lineages and selfrenewal-differentiation choices in NPCs.

2020-06-16 | GSE137783 | GEO

Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [ChIP-seq]

2020-06-16 | GSE137778 | GEO

Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation

Project description:Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation

| PRJNA573665 | ENA

Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [ChIP-seq]

Project description:Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation [ChIP-seq]

| PRJNA573655 | ENA

Ybx1 negatively regulates PRC2 to affect gene expression programs for neural lineage specification and neural progenitor self-renewal and differentiation

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

2020-06-16 | GSE137853 | GEO

YBX1 HITS-CLIP

Project description:In order to identify YBX1 binding sites on endogenous RNA, we performed HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Licatalosi D, et al. 2008, Nature 456:464-U22)

2015-05-08 | E-GEOD-63604 | biostudies-arrayexpress

YBX1 small-RNA HITS-CLIP

Project description:In order to identify YBX1 binding sites on tRNA fragments, we performed small-RNA HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Chi SW, et al. 2009, Nature 460:479)

2015-05-08 | E-GEOD-63597 | biostudies-arrayexpress

YBX1 interacting protein - C1QBP Negatively Regulates the Activation of Oncoprotein YBX1 in the Renal Cell Carcinoma As Revealed by Interactomics Analysis

Project description:The Y-box-binding protein 1 (YBX1) plays a critical role in tumorigenesis by promoting cell proliferation, overriding cell-cycle check points, and enhancing genomic instability. In this study, the interactome of YBX1 in renal cell carcinoma (RCC) was analyzed by coimmunoprecipitation and mass spectrometry to better understand its function and regulatory mechanism.

2015-01-30 | PXD001493 | Pride

Chip-chip from HCT116 cells with YBX1

Project description:YBX1 is a multifunctional protein involved in the control of transcription and translation. We identified YBX1 as an target of MEK/ERK signaling in colorectal cancer cell lines. We performed a ChIP-chip analysis of HCT116 cells to identify new potential target genes of YBX1. Comparison of input DNA fragments with fragments coprecipitated with YBX1 in HCT116 cells.

2010-10-09 | E-GEOD-18337 | biostudies-arrayexpress

YBX1-dependent hypoxia-induced modulation of gene expression

Project description:In order to identify YBX1-dependent targets that are modulated under hypoxic conditions, we used control and YBX1 knockdown cells grown under normoxia and hypoxia to profile gene expression levels. Control and YBX1-knockdown cells were grown and profiled under hypoxia and normoxia to identify YBX1-dependent hypoxia-induced target transcripts.

2015-05-08 | E-GEOD-63562 | biostudies-arrayexpress

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