Ybx1 binding sites and Ybx1-binding m5C sites in zebrafish embryo sample.
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ABSTRACT:
PROVIDER: PRJNA493828 | ENA |
REPOSITORIES: ENA
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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
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 | GSE120643 | GEO
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
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
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
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.
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Project description:m5C profiles in zebrafish embryo sample.
| PRJNA493829 | ENA
Project description:In order to identify YBX1 binding sites on endogenous RNA, we performed HITS-CLIP on endogenous YBX1
2015-05-08 | GSE63604 | GEO
Project description:In order to identify YBX1 binding sites on tRNA fragments, we performed small-RNA HITS-CLIP on endogenous YBX1
2015-05-08 | GSE63597 | GEO
Project description:In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by microarray profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets that are modulated due to tRF loss-of-function.
2015-05-08 | E-GEOD-63564 | biostudies-arrayexpress