Impact of depletion of groucho or notch on transcription in Drosophila intestinal stem cells (ISCs).
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA445697 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6898220.fastq.gz | Fastqsanger.gz | |||
| SRR6898221.fastq.gz | Fastqsanger.gz | |||
| SRR6898222.fastq.gz | Fastqsanger.gz | |||
| SRR6898223.fastq.gz | Fastqsanger.gz | |||
| SRR6898224.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To analysis impacts of groucho and notch on transcription in Drosophila ISCs by mRNA-seq. Methods: mRNA-seq of RNA extracted from FACS sorted Drosophila ISCs. Results: Groucho loss in ISCs leads to disruption of lateral inhibition,and knocking down notch in ISCs down-regulates expression of e(spl) factors.
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Project description:To examine whether IRF2, a negative regulator of IFN signaling, constitutively represses IFN signaling by binding IFN-inducible gene loci in ISCs, we performed a genome-wide chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) analysis of IRF2 in Lgr5 ISCs. We identified 381 binding peaks in these cells, including well-known IFN-inducible genes. Motif analysis showed significant enrichment of consensus-binding motifs for IRF transcription factors within these peaks. Within IRF2-occupied genes in ISCs, we identified 204 of experimentally validated IFN-inducible genes from Interferome database, and 10.8% of them were overlapped with the genes upregulated by type I IFN stimulation in ISCs. These findings indicated for the first time that IRF2 constitutively bound and repressed the sterile IFN signaling at the level of ISCs.
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Project description:We previously demonstrated that SRCAP regulates the self-renewal of ESCs and modulates lymphoid lineage commitment. We further validated that SRCAP was mainly distributed in liver, spleen and intestine by Northern blot. SRCAP was also highly expressed in Lgr5+ ISCs. We then sought to explore the physiological role of SRCAP in the regulation of self-renewal maintenance of ISCs.We then generated Srcapflox/flox mice through insertion of loxP sequences flanking at the exon5 of Srcap gene locus. We established Srcapflox/flox;Lgr5GFP-CreERT2 mice through crossing Srcapflox/flox mice with Lgr5GFP-CreERT2 mice. With administration of tamoxifen (TAM), Srcap was completely deleted in Lgr5+ ISCs. We identified that Srcap deficiency impairs the self-renewal of ISCs and intestinal epithelial regeneration. Through RNA-sequencing, we sough to identify the key gene regulated by SRCAP in ISC self-renewal.
2020-01-15 | GSE143657 | GEO
Project description:We previously demonstrated that SRCAP regulates the self-renewal of ESCs and modulates lymphoid lineage commitment. We further validated that SRCAP was mainly distributed in liver, spleen and intestine by Northern blot. SRCAP was also highly expressed in Lgr5+ ISCs. We then sought to explore the physiological role of SRCAP in the regulation of self-renewal maintenance of ISCs.We identified that Srcap deficiency impairs the self-renewal of ISCs and intestinal epithelial regeneration. Through SRCAP ChIP-sequencing, we sough to identify the key gene regulated by SRCAP in ISC self-renewal.
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Project description:Shavenbaby (Svb) transcription factor is involved in the differenciation of epidermal cells and the homeostasis of intestinal stem cells (ISCs). Svb is produced as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides SvbREP is processed into a shorter activator form (SvbACT) through partial proteasomal degradation of the REP domain. In ISCs, Pri triggers SvbREP to ACT maturation, while SvbREP form accumulates in differentiated enterocytes. The absence of Svb promote the apoptosis of the intestinal stem cells. In ISC, the ectopic expression of SvbREP form promote the differenciation and the SvbACT form overexpression promotes hyperplasia. (Al Hayel, et al 2020) Based on these functional analyses, Svb appears to control ISC survival and behavior, balancing proliferation and differentiation through a molecular switch between its 2 antagonistic isoforms. In this study, we determine the Svb target genes in ISCs. To this aim, we analyze the transcriptomes of ISCs upon modulation of Svb function.
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Project description:To analyze global gene-expression changes caused by IRF2 loss in ISCs, ISCs were prepared from Irf2fl/fl: Lgr5-EGFP-Ires-CreERT2(Irf2fl/fl: Lgr5ki) mice or Irf2fl/fl: Ah-Cre: Lgr5-EGFP-Ires-CreERT2 (Irf2AhcKO: Lgr5ki) mice 1 month after 5 consecutive days of βNF treatment. The Gene Ontology (GO) analysis indicated that the GO terms overrepresented among the genes upregulated in ISCs of βNF treated Irf2AhcKO: Lgr5ki mice compared with those of Irf2fl/fl: Lgr5ki mice included “immune system process”, “immune response”, and “cellular response to Interferon-beta”, all from the GOTERM_Biological Processes (BP) category. Because these GO_term inculded many IFN-inducibl genes, IFN signaling augumented in Irf2 deleted ISCs.
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Project description:Purpose: localized aberrant cell proliferation induced by activation of Yki in ISCs impairs muscle functions. To gain insight into the cross talk between intestine and muscle, we performed a transcriptomic analysis of thoracic muscles in ISC overproliferation flies. Methods: To extract total RNAs for RNA-Seq experiment, we used 10 thoraces dissected out from both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-act (Yki) flies incubated for 8 days at 29°C. After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down. Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using Illumina HiSeq2000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. Sequence reads were mapped back to the Drosophila genome (flybase genome annotation version r5.51) using Tophat. With the uniquely mapped reads, we quantified gene expression levels using Cufflinks (FPKM values). Next, we performed data normalization on the read counts and applied a negative binomial statistical framework using the Bioconductor package DESeq to quantify differential expression between experimental and control data. Results: Gene list enrichment analysis of the downregulated muscle transcriptome by ISCs Yki overexpressioin revealed a striking enrichment of multiple metabolic processes impinging on carbohydrate metabolism, amino acid metabolism, metabolism of vitamins and cofactors, and metabolism of xenobiotics by cytochrome P450. Interestingly, target genes of Foxo, a transcription factor inhibited by insulin/IGF signaling, are enriched in the upregulated muscle transcriptome of ISCs Yki overepxression flies. In particular, induction of InR and Thor, well-characterized targets of Foxo, are validated with qPCR. Conclusions: Our study represents ISCs overproliferation induced by Yki overepxression remotedly regulates muscle function and gene expression probally via modulation of insulin signaling in muscle. Our results show that RNA-seq offers a comprehensive evaluation of signaling network and biological process in organ communication. Thoraces mRNA profiles of both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-act (Yki) flies incubated for 8 days at 29°C were generated by deep sequencing, in replicate, using Illumina HiSeq2000.
2015-02-01 | E-GEOD-65325 | biostudies-arrayexpress
Project description:We have used ChIP followed by high throughput sequencing to profile the genome-wide recruitment of wildtype Groucho (Gro) at high resolution in BG3 Drosophila cells.
2022-09-15 | E-MTAB-12108 | biostudies-arrayexpress
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