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The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-cKO_RNAseq]

ABSTRACT: The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-cKO_RNAseq]

PROVIDER: PRJNA1064090 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27533446_1.fastq.gz	Fastqsanger.gz
	SRR27533446_2.fastq.gz	Fastqsanger.gz
	SRR27533447_1.fastq.gz	Fastqsanger.gz
	SRR27533447_2.fastq.gz	Fastqsanger.gz
	SRR27533448_1.fastq.gz	Fastqsanger.gz

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The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-cKO_RNAseq]

Project description:The reversible epitranscriptomic mark, 5-methylcytosine (m5C) modification, is implicated in numerous cellular processes, but its role in neuronal development remains largely unexplored. In this study, we discovered high expression of the m5C reader Ybx1 in the developing mouse cortex. To elucidate its role in cortical development, Ybx1 was deleted in mouse embryonic cortical neural stem cells (NSCs). Interestingly, the deletion of Ybx1 led to perinatal mortality in mice, along with abnormal cortical development. Cortical progenitor cells lacking Ybx1 exhibited impaired proliferation and differentiation. Multi-omics analysis identified the target mRNAs of Ybx1, which encode the key cell cycle regulatory proteins, such as cyclin D2 (Ccnd2). Ybx1 was found to regulate the stability of its target transcripts. Both knockdown and overexpression of Ybx1 targets via in utero electroporation confirmed that they mediated the Ybx1 regulation of proliferation and differentiation of neural precursor cells. Further mechanistic analysis showed that deletion of Ybx1 resulted in the blocking of G1 to S phase transition in the cortical progenitor cells. This study highlights the crucial function of the m5C reader protein Ybx1 in promoting cell cycle progression of the embryonic cortical progenitors, essential for proper cortical development.

2025-04-19 | GSE253129 | GEO

The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-KD_RNAseq]

2025-04-19 | GSE253128 | GEO

The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-KD_RNAseq]

Project description:The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-KD_RNAseq]

| PRJNA1064087 | ENA

The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E18.5-cKO_RNAseq]

2025-04-19 | GSE253130 | GEO

The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [RIP-seq]

2025-04-19 | GSE253131 | GEO

Anti-Ybx1 RIP-seq to identify target mRNAs of Ybx1 in E13.5 DRG [RIP-seq]

Project description:In order to identify the target mRNAs of the m5C reader protein Ybx1, we carried out anti-Ybx1 RNA Immunoprecipitation(RIP) followed by RNA-sequencing to find out mRNAs that can directly bind by Ybx1. Using EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from E13.5 wildtype mouse DRGs was pulled down by rabbit monoclonal anti-Ybx1 (abcam) and sequenced on IIIumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm39) using BWA mem (v 0.7.12). After peak calling using MACS2 (version 2.1.0) software, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed. Fold enrichment greater than 2 was considered to be enriched. Finally, 2 biological repilicates of anti-Ybx1 RIP-seq identified 2487 transcripts. This study provides a gene list which shows mRNA binding with Ybx1 in mouse DRGs.

2024-11-15 | GSE254854 | GEO

The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression.

Project description:The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression.

| PRJNA1064077 | ENA

The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [RIP-seq]

Project description:The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [RIP-seq]

| PRJNA1064088 | ENA

The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E18.5-cKO_RNAseq]

Project description:The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E18.5-cKO_RNAseq]

| PRJNA1064089 | ENA

m5C-MeRIP-seq of HHL5 cells

Project description:We discovered the YBX1 in the lipid-induced particles assembled by DDX49, YBX1 is an m5C reader and constitutively associates with Timp2 mRNA in hepatocytes, we examined whether their association was dependent on the m5C modification of Timp2 mRNA, then we performed m5C-MeRIP-seq.

2025-06-20 | GSE299800 | GEO

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