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A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [DamID-Seq]

ABSTRACT: A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [DamID-Seq]

PROVIDER: PRJNA871226 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21146071.fastq.gz	Fastqsanger.gz
	SRR21146072.fastq.gz	Fastqsanger.gz
	SRR21146073.fastq.gz	Fastqsanger.gz
	SRR21146074.fastq.gz	Fastqsanger.gz
	SRR21146075.fastq.gz	Fastqsanger.gz

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A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [DamID-Seq]

Project description:Enteroendocrine cells (EEs) represent a heterogeneous cell population in intestine and exert endocrine functions by secreting a diverse array of neuropeptides. Although many transcription factors (TFs) required for specification of EEs have been identified in both mammals and Drosophila, it is not understood how these TFs work together to generate this considerable subtype diversity. Here we show that EE diversity in adult Drosophila is generated via an “additive hierarchical TF cascade”. Specifically, a combination of a master TF, a secondary-level TF and a tertiary-level TF constitute a “TF code” for generating EE diversity. We also discover a high degree of post-specification plasticity of EEs, as changes in the code—including as few as one distinct TF—allow efficient switching of subtype identities. Our study thus reveals a hierarchically-organized TF code that underlies EE diversity and plasticity in Drosophila, which can guide investigations of EEs in mammals and inform their application in medicine.

2022-10-18 | GSE211629 | GEO

A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila

Project description:A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila

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A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [RNA-Seq]

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A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [RNA-Seq]

Project description:A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila [RNA-Seq]

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A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila.

Project description:Enteroendocrine cells (EEs) represent a heterogeneous cell population in intestine and exert endocrine functions by secreting a diverse array of neuropeptides. Although many transcription factors (TFs) required for specification of EEs have been identified in both mammals and Drosophila, it is not understood how these TFs work together to generate this considerable subtype diversity. Here we show that EE diversity in adult Drosophila is generated via an "additive hierarchical TF cascade". Specifically, a combination of a master TF, a secondary-level TF and a tertiary-level TF constitute a "TF code" for generating EE diversity. We also discover a high degree of post-specification plasticity of EEs, as changes in the code-including as few as one distinct TF-allow efficient switching of subtype identities. Our study thus reveals a hierarchically-organized TF code that underlies EE diversity and plasticity in Drosophila, which can guide investigations of EEs in mammals and inform their application in medicine.

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MicroRNA-7 regulates the plasticity of the enteroendocrine lineage

Project description:MicroRNA-7 regulates the plasticity of the enteroendocrine lineage

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A hierarchical transcription factor cascade regulates enteroendocrine cell diversity and plasticity in Drosophila

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-10-18 | GSE211632 | GEO

Identification of functional enteroendocrine regulators by real-time single-cell differentiation mapping

Project description:Homeostatic regulation of the intestinal enteroendocrine lineage hierarchy is a poorly understood process. We resolved transcriptional changes during enteroendocrine differentiation in real-time at single-cell level using a novel knock-in allele of Neurog3, the master regulator gene briefly expressed at the onset of enteroendocrine specification. A bi-fluorescent reporter, Neurog3Chrono, measures time from the onset of enteroendocrine differentiation and enables precise positioning of single-cell transcriptomes along an absolute time axis. This approach yielded a definitive description of the enteroendocrine hierarchy and its sub-lineages, uncovered differential kinetics between sub-lineages, and revealed time-dependent hormonal plasticity in enterochromaffin and L-cells. The time-resolved map of transcriptional changes predicted multiple novel molecular regulators. Nine of these were validated by conditional knockout in mice or CRISPR-modification in intestinal organoids. Six novel candidate regulators (Sox4, Rfx6, Tox3, Myt1, Runx1t1 and Zcchc12) yielded specific enteroendocrine phenotypes. Our time-resolved single cell transcriptional map presents a rich resource to unravel enteroendocrine differentiation.

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Project description:We generated knock-in mice expressing GFP under the control of the endogenous GIP (Glucose-dependent Insulinotropic Polypeptide) promoter that enable the isolation of a purified population of small intestine K cells. Using RNA-Seq, we comprehensively characterized the transcriptomes of GIP-GFP cells as well as the entire enteroendocrine lineage derived from Neurogenin3 (Ngn3)-expressing progenitors. We interrogated the whole transcriptome of FACS-isolated small intestine GIPGFP cells using high-throughput mRNA sequencing. We also obtained the global gene expression patterns of the entire enteroendocrine cell lineage as well as the non-enteroendocrine cell population, comprising enterocytes, goblet cells and Paneth cells. To achieve this, small intestine epithelial cells from male mice resulting from the breeding of Neurogenin3 (Ngn3)-Cre mice with ROSA26-LoxP-STOP-LoxP-tomato indicator mice were isolated based on Tomato fluorescence and negative staining for CD45. Due to the small cell numbers, we constructed each of the three RNA-Seq libraries (GIPGFP, Ngn3TOMATO, and Ngn3-) using a pool of equal amounts of individual RNA samples without RNA amplification.

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Profiling of Esg genomic binding in the Drosophila midgut with DamID

Project description:Tissue stem cells divide asymmetrically to self-renew and generate differentiated progeny to maintain tissue homeostasis. Escargot (Esg) is a transcriptional repressor that is expressed in multiple stem cell populations in Drosophila melanogaster. Reduced esg function in intestinal stem cells (ISCs) causes a loss of ISCs and a biased differentiation of the daughter enteroblasts (EBs) toward the enteroendocrine (EE) cell fate. Loss of esg leads to an upregulation of differentiation factors and reduced Notch activity within EBs, indicating that Esg is a pivotal regulator of homeostasis in the intestine, supporting self-renewal to maintain a healthy stem cell pool as well as differentiation of progenitor cells. To identify potential transcriptional targets that mediate these phenotypes, in vivo DamID was used to generate the data deposited herein. 3 biological relicates were performed for Esg (with one dye-swap).

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