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

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

PROVIDER: PRJNA1064087 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27533141_1.fastq.gz	Fastqsanger.gz
	SRR27533141_2.fastq.gz	Fastqsanger.gz
	SRR27533142_1.fastq.gz	Fastqsanger.gz
	SRR27533142_2.fastq.gz	Fastqsanger.gz
	SRR27533143_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 [RIP-seq]

2025-04-19 | GSE253131 | GEO

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 [E13.5-cKO_RNAseq]

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

| PRJNA1064090 | ENA

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

Ybx1 binding sites and Ybx1-binding m5C sites in zebrafish embryo sample.

Project description:The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic-driven programing. However, how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m5C) in zebrafish early embryos, we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box-binding protein 1 (Ybx1) prefers to recognizing m5C-modified mRNAs through p-p interaction with a key residue Trp45 in its cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m5C-dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation-regulated maternal mRNA stability during zebrafish MZT, highlighting the critical role of m5C mRNA methylation in early development.

2019-08-07 | GSE120646 | GEO

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