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The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq and scATAC-seq]

ABSTRACT: The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq and scATAC-seq]

PROVIDER: PRJNA803442 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17884000_1.fastq.gz	Fastqsanger.gz
	SRR17884000_2.fastq.gz	Fastqsanger.gz
	SRR17883997_1.fastq.gz	Fastqsanger.gz
	SRR17883997_2.fastq.gz	Fastqsanger.gz
	SRR17883998_1.fastq.gz	Fastqsanger.gz

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The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition

Project description:The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition

| PRJNA803437 | ENA

The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq and scATAC-seq]

Project description:Direct reprogramming of fibroblasts into induced cardiomyocytes (iCMs) holds great promise for heart regeneration. Although great progress has been made in understanding the transcriptional and epigenetic mechanisms of iCM reprogramming, its translational regulation remains largely unexplored. Here we characterized the translational landscape of iCM reprogramming using integrative ribosome and transcriptomic profiling, and showed extensive translatome re-patterning during fibroblast conversion into iCM. Loss of function screening for translational regulators uncovered Ybx1 as a critical barrier to iCM induction. Knockdown of Ybx1 dramatically improved the efficiency and quality of iCM reprogramming. Mechanistically, Ybx1 directly bound the transcripts of Srf and Baf60c, both of which mediated, at least partially, the repressive effect of Ybx1 on iCM generation.and Depletion of Ybx1 de-repressed the translation of its targets including SRF and Baf60c. Interestingly, upon removing Ybx1, Tbx5 alone could reprogram fibroblasts into iCMs that exhibit classic iCM molecular features and reprogramming trajectories revealed by our single cell dual-omics. In sum, we presented here a global view of translatome dynamics of cardiac reprogramming and identified a novel translational barrier, Ybx1, to iCM generation. Removing this barrier allowed the single factor mediated iCM reprogramming.

2023-08-24 | GSE196125 | GEO

The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq]

Project description:The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq]

| PRJNA994502 | ENA

The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq]

2023-08-24 | GSE237267 | GEO

The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [Ribo-seq and RNA-seq]

2023-08-24 | GSE196124 | GEO

The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [Ribo-seq and RNA-seq]

Project description:The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [Ribo-seq and RNA-seq]

| PRJNA803443 | ENA

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

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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