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Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 (RNA-seq and Ribo-seq)

ABSTRACT: Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 (RNA-seq and Ribo-seq)

PROVIDER: PRJNA871254 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21140654_1.fastq.gz	Fastqsanger.gz
	SRR21140654_2.fastq.gz	Fastqsanger.gz
	SRR21140655_1.fastq.gz	Fastqsanger.gz
	SRR21140655_2.fastq.gz	Fastqsanger.gz
	SRR21140656_1.fastq.gz	Fastqsanger.gz

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Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density

Project description:mRNAs are generally assumed to be loaded instantly with ribosomes upon entry into the cytoplasm. To measure ribosome density on nascent mRNA, we developed nascent Ribo-Seq (nRibo-Seq) by combining Ribo-Seq with progressive 4-thiouridine labelling. In mouse macrophages, we experimentally determined, for the first time, the lag between the appearance of nascent RNA and its association with ribosomes, which was calculated to be 20 - 22 min for bulk mRNA, and approximated the time it takes for mRNAs to be fully loaded with ribosomes to be 41 - 44 min. Notably, ribosomal loading time is adapted to gene function as rapid loading was observed with highly regulated genes. The lag and ribosomal loading time correlate positively with ORF size and mRNA half-life, and negatively with tRNA adaptation index. Similar results were obtained in mouse embryonic stem cells, where the lag in ribosome loading was even more pronounced with 35 - 38 min. We validated our measurements after stimulation of macrophages with lipopolysaccharide, where the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments. Uncoupling is stronger for mRNAs with long ORFs or half-lives, a finding we also confirmed at the level of protein production by nascent chain proteomics. As a consequence of the lag in ribosome loading, ribosome density measurements are distorted when performed under conditions where mRNA levels are far from steady state expression, and transcriptional changes affect ribosome density in a passive way. This study uncovers an unexpected and considerable lag in ribosome loading, and provides guidelines for the interpretation of Ribo-Seq data taking passive effects on ribosome density into account.

2021-06-22 | PXD026828 | Pride

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 (RNA-seq and Ribo-seq)

Project description:Purpose: To systematically investigate the molecular mechanisms resulting from Mycn loss-of-function. Methods: Approximately 30 mycn mutant or WT zebrafish embryos at 72 hpf (hours post fertilization) were harvested . Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000074) according to the manufacturer’s protocol for 10000 cells recovery. Results: More than 3,000 genes showed reduced tranlation efficiency in Mycn mutant. Conclusions: mTOR signaling was reduced in Mycn mutant.

2022-08-26 | GSE211652 | GEO

Ribo Mega-SEC Provides a Rapid, Efficient and Reproducible Analysis of Mammalian Polysomes and Ribosomal Subunits

Project description:We describe Ribo Mega-SEC, a powerful approach for the separation and biochemical analysis of mammalian polysomes and ribosomal subunits using Size Exclusion Chromatography and uHPLC, which was achieved within 15 min from sample injection to fraction collection. Ribo Mega-SEC reproducibly shows translating ribosomes exist predominantly in polysome complexes in extracts isolated from human cell lines and mouse liver tissue, which alter in response to starvation. Ribo Mega-SEC provides a rapid, efficient, convenient and highly reproducible method for studying functional translation complexes and is easily combined with high-through put analysis such as proteomics and RNA-Seq, or with structural analysis using electron microscopy. We propose that Ribo Mega-SEC analysis is an accessible alternative to traditional polysome profiling using sucrose density gradients.

2018-08-10 | PXD008913 | Pride

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [bulk RNA-seq]

Project description:Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [bulk RNA-seq]

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Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1

Project description:Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1

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Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [single-cell RNA-seq]

Project description:Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [single-cell RNA-seq]

| PRJNA789277 | ENA

LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (RIP-Seq)

Project description:High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we show that LIN28B expression is associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7 independent enrichment of transcripts encoding components of the translational and ribosomal apparatus, particularly those with higher adenine/uridine (AU)-content, and depletion of transcripts of neuronal developmental programs. We further show that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrate that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a post-transcriptional driver of the metastatic phenotype.

2022-09-30 | GSE183336 | GEO

LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (RNA-Seq)

Project description:High expression of LIN28B is associated with aggressive malignancy and poor survival. Here, probing MYCN-amplified neuroblastoma as a model system, we show that LIN28B expression is associated with enhanced cell migration in vitro and invasive and metastatic behavior in murine xenografts. Sequence analysis of the polyribosome fraction of LIN28B-expressing neuroblastoma cells revealed let-7 independent enrichment of transcripts encoding components of the translational and ribosomal apparatus, particularly those with higher Adenine/Uridine (AU)-content, and depletion of GC-rich transcripts of neuronal developmental programs. We further show that LIN28B utilizes both its cold shock and zinc finger RNA binding domains to preferentially interact with MYCN-induced transcripts of the ribosomal complex, enhancing their translation. These data demonstrate that LIN28B couples the MYCN-driven transcriptional program to enhanced ribosomal translation, thereby implicating LIN28B as a post-transcriptional driver of the metastatic phenotype.

2022-09-30 | GSE158320 | GEO

LIN28B alters ribosomal dynamics to promote metastasis in MYCN-driven malignancy (Polysome sequencing)

2022-09-30 | GSE183335 | GEO

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 [bulk RNA-seq]

Project description:Purpose: To identify differential expressed genes for loss of function of Mycn in zebrafish Methods: wild-type and mycn mutant zebrafish embryos were collected for RNA sequencing at 48 hpf (hours post fertilisation) and 72 hpf Results: We found 85 (overlapped) down-regulated genes in mycn mutant embryos at 48 hpf and 72 hpf (padj < 0.1, log2 fold change < 0) Conclusions: 85 down-regulated genes were identified

2021-12-17 | GSE191001 | GEO

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