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Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity

ABSTRACT: Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity

PROVIDER: PRJNA762678 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15861909.fastq.gz	Fastqsanger.gz
	SRR15861910.fastq.gz	Fastqsanger.gz
	SRR15861911.fastq.gz	Fastqsanger.gz
	SRR15861912.fastq.gz	Fastqsanger.gz
	SRR15861913.fastq.gz	Fastqsanger.gz

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Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity

Project description:The role of Processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive Enterocytes (ECs), harbor P-bodies that contain Drosophila orthologs of mammalian P-body components DDX6, EDC3, EDC4 and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, including Patr-1, a gene necessary for P-body assembly. Loss of Patr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate translation and expression of EC-fate gene nubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a coordinated P-body dependent, translational and transcriptional repression program that maintains a defined set of in vivo stem cells in a state primed for differentiation.

2021-12-06 | GSE183996 | GEO

Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity.

Project description:The role of processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive enterocytes (ECs), harbor P-bodies that contain Drosophila orthologs of mammalian P-body components DDX6, EDC3, EDC4, and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, including Patr-1, a gene necessary for P-body assembly. Loss of Patr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate expression of EC-fate gene nubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a P-body-dependent repression activity that coordinates with known transcriptional repression programs to maintain a population of in vivo stem cells in a state primed for differentiation.

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Project description:Post-transcriptional regulation is pivotal in guiding the gene expression programs that instruct cell fate decisions. Recent studies emphasize the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in the context of cell fate specification are unknown. In this study, we profiled the coding and non-coding transcriptome within intact biomolecular condensates known as P-bodies in diverse developmental contexts and vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of RNAs encoding key cell fate specifiers. Notably, P-body contents did not directly reflect gene expression profiles for a given cell type, but rather were enriched for transcripts characteristic of the preceding developmental stage, which are translationally suppressed and stored within P-bodies. We demonstrate that the forced degradation of P-bodies stimulates the translation of transcripts encoding fate-instructive factors, ultimately re-activating a totipotency transcriptional program in human and mouse pluripotent cells. Mechanistically, microRNAs (miRNAs) facilitate the sequestration of specific RNAs into P-bodies in a context-dependent manner. Accordingly, perturbing AGO2, alternative polyadenylation, and miRNA function profoundly reshapes the RNA content of P-bodies and alters cell fate. Furthermore, we show that adding a miRNA target sequence is sufficient to redirect transcripts to P-bodies and influence stem cell self-renewal. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species.

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