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Analysis of PDCD4 knockdown effects by high throughput sequencing of a human epithelial cell line

ABSTRACT: Analysis of PDCD4 knockdown effects by high throughput sequencing of a human epithelial cell line

PROVIDER: PRJNA576260 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10240635.fastq.gz	Fastqsanger.gz
	SRR10240636.fastq.gz	Fastqsanger.gz
	SRR10240637.fastq.gz	Fastqsanger.gz
	SRR10240638.fastq.gz	Fastqsanger.gz
	SRR10240639.fastq.gz	Fastqsanger.gz

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Analysis of PDCD4 knockdown effects by high throughput sequencing of a human epithelial cell line

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Project description:PDCD4 is a multifunctional RNA binding protein which has tumour suppressor function. To more fully understand how dysregulation of this protein contributes to carcinogenesis we have carried out a comprehensive analysis of the role of PDCD4 in RNA metabolism in untransformed epithelial cells. We show that PDCD4 predominantly localises in the nucleus, where it interacts with proteins involved in a range of different RNA metabolic processes. We find that PDCD4 knockdown is associated with significant changes in either the expression or splicing of a number of transcripts, although it appears to have an indirect role in splicing. We identified the RNA targets of PDCD4 using iCLIP and observed an enrichment in binding to transcripts encoding cell adhesion and structural proteins. Consistent with these data, we show that PDCD4 acts as a general regulator of cell adhesion, which in a tumour setting would increase the metastatic potential of cells, and demonstrate that the nuclear localisation of PDCD4 is crucial in this process. Overall, the information obtained in untransformed cells provides new perspective for the role of PDCD4 as a tumour suppressor.

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Project description:Activity-dependent gene expression is critical for synapse development and plasticity. To elucidate novel mechanisms linking neuronal activity to changes in transcription, we compared the nuclear proteomes of tetrodotoxin-silenced and bicuculline-stimulated cultured neurons using nuclear-localized APEX2 proximity biotinylation and mass spectrometry. The tumor suppressor protein PDCD4 was enriched in the nuclear proteome of silenced neurons, and PDCD4 levels rapidly decreased in the nucleus and cytoplasm of stimulated neurons. The activity-dependent decrease of PDCD4 was prevented by inhibitors of both PKC and proteasome activity and by a phospho-incompetent mutation of Ser71 in the βTRCP ubiquitin ligase-binding motif of PDCD4. We compared the activity-dependent transcriptomes of neurons expressing wildtype or degradation-resistant (S71A) PDCD4. We identified 91 genes as PDCD4 targets at the transcriptional level, including genes encoding proteins critical for synapse formation, remodeling, and transmission. Our findings indicate that regulated degradation of nuclear PDCD4 facilitates activity-dependent transcription in neurons.

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