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Heading towards a dead end: the role of DND1 in germ line differentiation of human iPSCs

ABSTRACT: Heading towards a dead end: the role of DND1 in germ line differentiation of human iPSCs

PROVIDER: PRJNA730018 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14546029_1.fastq.gz	Fastqsanger.gz
	SRR14546029_2.fastq.gz	Fastqsanger.gz
	SRR14546030_1.fastq.gz	Fastqsanger.gz
	SRR14546030_2.fastq.gz	Fastqsanger.gz
	SRR14546031_1.fastq.gz	Fastqsanger.gz

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Heading towards a dead end: the role of DND1 in germ line differentiation of human iPSCs

Project description:We knocked out DND1 in human iPSCs and analysed its role in pluripotency and differentiation. We showed that general pluripotency gene expression is not affected, but KO iPSCs differentiate less efficiently towards PGC-like cells and remaining PGCLCs show reduced expression of NANOS3 and PRDM1.

2021-10-20 | GSE174464 | GEO

Heading towards a dead end: the role of DND1 in germ line differentiation of human iPSCs

Project description:The DND microRNA-mediated repression inhibitor 1 (DND1) is a conserved RNA binding protein (RBP) and plays an important role in survival and maintenance of primordial germ cells (PGCs) and the development of the male germline in zebrafish and mice. It was shown to be expressed in human pluripotent stem cells (PSCs), PGCs, and spermatogonia, but little is known about its specific role in pluripotency and human germline development. Here we use CRISPR/Cas mediated knockout and PGC-like cell (PGCLC) differentiation in human iPSCs to analyse if DND1 (1) plays a role in maintaining pluripotency and (2) in specification of PGCLCs. We generated several clonal lines with biallelic loss of function mutations and analysed their potential to differentiate towards PGCLCs and their gene expression on RNA and protein level via bulk RNA sequencing and mass spectrometry. The generated knockout iPSCs showed no differences in pluripotency gene expression, proliferation nor trilineage differentiation potential, but yielded reduced numbers o PGCLCs compared to their parental iPSCs. RNAseq analysis in PGCLCs showed significantly reduced expression of genes associated with cellular developmental processes and cell differentiation in knockout cells, including known markers for PGCs (NANOS3, SOX17, PRDM1, EPCAM) and naïve pluripotency (TFCP2L, DNMT3L).

2021-12-10 | PXD023802 | Pride

Heading towards a dead end: The role of DND1 in germ line differentiation of human iPSCs.

Project description:The DND microRNA-mediated repression inhibitor 1 (DND1) is a conserved RNA binding protein (RBP) that plays important roles in survival and fate maintenance of primordial germ cells (PGCs) and in the development of the male germline in zebrafish and mice. Dead end was shown to be expressed in human pluripotent stem cells (PSCs), PGCs and spermatogonia, but little is known about its specific role concerning pluripotency and human germline development. Here we use CRISPR/Cas mediated knockout and PGC-like cell (PGCLC) differentiation in human iPSCs to determine if DND1 (1) plays a role in maintaining pluripotency and (2) in specification of PGCLCs. We generated several clonal lines carrying biallelic loss of function mutations and analysed their differentiation potential towards PGCLCs and their gene expression on RNA and protein levels via RNA sequencing and mass spectrometry. The generated knockout iPSCs showed no differences in pluripotency gene expression, proliferation, or trilineage differentiation potential, but yielded reduced numbers of PGCLCs as compared with their parental iPSCs. RNAseq analysis of mutated PGCLCs revealed that the overall gene expression remains like non-mutated PGCLCs. However, reduced expression of genes associated with PGC differentiation and maintenance (e.g., NANOS3, PRDM1) was observed. Together, we show that DND1 iPSCs maintain their pluripotency but exhibit a reduced differentiation to PGCLCs. This versatile model will allow further analysis of the specific mechanisms by which DND1 influences PGC differentiation and maintenance.

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Arabidopsis dnd1

Project description:Transcript profiling of dnd1 mutant grown in control condition.

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Transcriptome changes in leaves of the DEFENSE NO DEATH 1 (DND1) silenced potato plants

Project description:Silencing of DND1 in potato leads to resistance to late blight, powdery mildew and Botrytis cinerea. At the same time, however, it reduces plant growth and causes leaf necrosis. To get knowledge on the molecular events behind the pleiotropic effect of DND1 downregulation in potato transcriptome analysis were performed on three DND1 silenced lines in comparison with the potato cultivar ‘Désirée’ as a wild-type.

2024-10-22 | E-MTAB-13824 | biostudies-arrayexpress

Gene expression analysis of control and Dnd1-cKO germ cells at E11.5.

Project description:The present investigation was to identify transcriptomic changes of control and Dnd1-cKO PGCs at E11.5 by RNA-seq analysis. We identified 181 upregulated and 141 downregulated genes in Dnd1-cKO PGCs.

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Project description:DEAD

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Gene expression analysis of control and Dnd1-cKO germ cells at E12.5 and E13.5.

Project description:The present investigation was to identify transcriptomic changes of control and Dnd1-cKO PGCs at E12.5 and E13.5 by microarray comparison. We identified 1470 upregulated and 924 downregulated genes in Dnd1-cKO PGCs.

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DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using ChIP-seq, we determined the sites where HTP-tagged Dbp2 associates with chromatin. ChIP-seq of Srp2-HTP is included as a reference protein that is known to associate with transcribing RNA polymerase II (RNAPII).

2024-06-30 | E-MTAB-13712 | biostudies-arrayexpress

DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation - III

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using RNA-seq, we determined RNA expression profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were harvested at the beginning (t0) or the end (t5 or t9) of shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before harvesting.

2024-06-30 | E-MTAB-13717 | biostudies-arrayexpress

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