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

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

PROVIDER: PRJNA493828 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7942635_1.fastq.gz	Fastqsanger.gz
	SRR7942635_2.fastq.gz	Fastqsanger.gz
	SRR7942636_1.fastq.gz	Fastqsanger.gz
	SRR7942636_2.fastq.gz	Fastqsanger.gz
	SRR7942637_1.fastq.gz	Fastqsanger.gz

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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

Transcriptomics analysis of gene expression in wide type, ybx1 MO, pabpc1a MO zebrafish embryo sample.

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Integrated analysis based on RNA immunoprecipitation sequencing (RIP-seq) and m5C methylated RNA immunoprecipitation and sequencing (MeRIP-seq) assays to identify the target genes of NSUN2/YBX1-m5C axis in ESCC progression

Project description:The modification and recognition of 5-methylcytosine (m5C) are involved in the initiation and progression of various tumor types. However, the precise role and potential mechanism of Y-box-binding protein 1 (YBX1) in esophageal squamous cell carcinoma (ESCC) remains unclear. Here, we found that YBX1 was frequently upregulated in ESCC compared with matched nontumor tissues. Gain- and loss-of-function assays showed that YBX1 promoted the proliferation and metastasis of ESCC cells both in vitro and in vivo. Functional studies revealed that NOP2/Sun RNA methyltransferase family member 2 (NSUN2) is a critical RNA methyltransferase that facilitates YBX1-mediated ESCC progression. Mechanistically, integrated analysis based on RNA immunoprecipitation sequencing (RIP-seq) and m5C methylated RNA immunoprecipitation and sequencing (MeRIP-seq) assays identified spermine oxidase (SMOX) as a target gene containing an m5C site in its coding sequence (CDS) region, which coincided well with the binding site of YBX1. Overexpression of SMOX-WT but not SMOX-Mut partially restored the proliferation and invasion ability of ESCC cells curbed by YBX1 knockdown. Moreover, YBX1 activated the mTORC1 signaling pathway by stabilizing SMOX mRNA. Our study revealed that YBX1 promotes ESCC development by stabilizing SMOX mRNA in an m5C-dependent manner, thus providing a valuable therapeutic target for ESCC.

2024-06-05 | GSE249045 | 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)

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Drosophila YBX1 homolog YPS promotes ovarian germline stem cell development by preferentially recognizing 5-methylcytosine RNAs

Project description:5-Methylcytosine (m5C) is one of the most abundant RNA modifications, but its function in adult stem cell development remains poorly defined. This study shows that Ypsilon schachtel (YPS) promotes germ line stem cell (GSC) maintenance, proliferation, and differentiation in the adult Drosophila ovary by preferentially binding to m5C-containing RNAs. Highly conserved cold-shock domains (CSDs) of YPS and its human homolog Y box binding protein 1 (YBX1) exhibit preferential binding to m5C-containing RNAs through hydrophobic interactions. Human YBX1 can functionally replace YPS to promote GSC development in the Drosophila ovary, and overexpressing RNA-binding–defective YBX1 and YPS mutant proteins disrupts normal GSC development. Thus, this study provides insight into the importance of m5C RNA modification in adult stem cell development.

2020-02-03 | GSE139828 | GEO

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Project description:EV-packaged PIAT mediates EGR1, NTRK1 and SMAD7 mRNA stability in a YBX1-dependent manner. To explore whether YBX1 enhances EGR1, NTRK1 and SMAD7 mRNA stability in an m5C-dependent manner, we conducted m5C-seq in PANC-1 cells to map the m5C methylome of PANC-1 cells treated with CAF-derived EVs.

2024-04-20 | GSE263948 | GEO

m5C profiles in zebrafish embryo sample.

Project description:m5C profiles in zebrafish embryo sample.

| PRJNA493829 | ENA

YBX1 HITS-CLIP

Project description:In order to identify YBX1 binding sites on endogenous RNA, we performed HITS-CLIP on endogenous YBX1

2015-05-08 | GSE63604 | 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

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