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Differential ribosome engagement profiling between undifferentiated and neuron-differentiated P19 cells

ABSTRACT: Differential ribosome engagement profiling between undifferentiated and neuron-differentiated P19 cells

PROVIDER: PRJNA887109 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21803821.fastq.gz	Fastqsanger.gz
	SRR21803822.fastq.gz	Fastqsanger.gz
	SRR21803823.fastq.gz	Fastqsanger.gz
	SRR21803824.fastq.gz	Fastqsanger.gz
	SRR21803825.fastq.gz	Fastqsanger.gz

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Differential ribosome engagement profiling between undifferentiated and neuron-differentiated P19 cells

Project description:Translation is tightly regulated during differentiation. To gain insights into the mechanism regulating translational activity at the transcript level, we performed Ribosome Profiling of undifferentiated and neuron-differentiated P19 cells. Relative changes in translational activity between the undifferentiated and differentiated cells show an increase in the translational activity of the transcripts encoding for ribosomal proteins compared to the rest of the transcriptome. Thus, in this differentiation system, the biogenesis of the translational machinery is tightly controlled at the translational level.

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Project description:SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro. P19 embryonic carcinoma (EC) cells, induced to form cardiomyocytes in vitro - undifferentiated cells, day 3+0.5 and day 3+3.0 of differentiation protocol. Keywords = EC cells, P19, differentiation, cardiomyocytes Keywords: time-course

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Characterization of the survival motor neuron (SMN) promoter provides evidence for complex combinatorial regulation in undifferentiated and differentiated P19 cells.

Project description:There exist two SMN (survival motor neuron) genes in humans, the result of a 500 kb duplication in chromosome 5q13. Deletions/mutations in the SMN1 gene are responsible for childhood spinal muscular atrophy, an autosomal recessive neurodegenerative disorder. While the SMN1 and SMN2 genes are not functionally equivalent, up-regulation of the SMN2 gene represents an important therapeutic target. Consequently, we exploited in silico, in vitro and in vivo approaches to characterize the core human and mouse promoters in undifferentiated and differentiated P19 cells. Phylogenetic comparison revealed four highly conserved regions that contained a number of cis-elements, only some of which were shown to activate/repress SMN promoter activity. Interestingly, the effect of two Sp1 cis-elements varied depending on the state of P19 cells and was only observed in combination with a neighbouring Ets cis-element. Electrophoretic mobility-shift assay and in vivo DNA footprinting provided evidence for DNA-protein interactions involving Sp, NF-IL6 and Ets cis-elements, whereas transient transfection experiments revealed complex interactions involving these recognition sites. SMN promoter activity was strongly regulated by an NF-IL6 response element and this regulation was potentiated by a downstream Ets element. In vivo results suggested that the NF-IL6 response must function either via a protein-tethered transactivation mechanism or a transcription factor binding an upstream element. Our results provide strong evidence for complex combinatorial regulation and suggest that the composition or state of the basal transcription complex binding to the SMN promoter is different between undifferentiated and differentiated P19 cells.

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