Ontology highlight
ABSTRACT:
PROVIDER: PRJNA993436 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25230114_1.fastq.gz | Fastqsanger.gz | |||
| SRR25230114_2.fastq.gz | Fastqsanger.gz | |||
| SRR25230115_1.fastq.gz | Fastqsanger.gz | |||
| SRR25230115_2.fastq.gz | Fastqsanger.gz | |||
| SRR25230116_1.fastq.gz | Fastqsanger.gz |
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Project description:Here we show that the Drosophila nuclear receptor DHR39 is necessary for male reproduction and acts as a global regulator of accessory gland gene expression. Mutants for the DHR39 transcription factor are sterile, with the majority of accessory gland genes expressed at reduced levels. Specific depletion of DHR39 within the accessory gland is sufficient to reduce male fecundity and accessory gland gene expression. Restoration of DHR39 in the accessory gland of DHR39 mutants rescues this sterility and transcriptional reduction. We conclude that DHR39 is a key regulator of most accessory gland genes, including ovulin and sex peptide, and is necessary for male fertility.
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Project description:Comparative accessory gland transcriptomics in Drosophila
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Project description:The Drosophila melanogaster male accessory gland (AG) is crucial for reproductive success, producing seminal fluid proteins that impact female post-mating behavior and physiology. To understand the regulatory networks governing accessory gland function, we conducted a bulk RNA sequencing (RNA-Seq) study to analyze the effects of overexpressing three key regulatory genes: dMyc, Yorkie (Yki), and the E2F-Dp heterodimer, compared to wild-type (WT) controls. We found upregulated and downregulated genes in each condition compared to controls, affecting immune response, cell cycle, stress response, and reproductive functions. In both Yki constitutively active, E2F+Dp and dMyc, E2F+DP conditions, several genes known to be involved in wound healing and tumorigenic models in flies were upregulated, including JNK signaling targets Ets21C, MMP1, puckered, and Jak/STAT signaling pathway ligands upd2 and upd3. Conversely, accessory gland-specific genes, such as many Accessory Gland Proteins (Acps), and genes involved in fertility, mating behavior, and sperm competition were downregulated. There was a strong overlap between the Yki constitutively active, E2F+Dp and dMyc, E2F+Dp gene expression signatures, converging on genes commonly misregulated in proliferative tumor models in various larval tissues, including imaginal discs and brains. This study provides insights into the molecular mechanisms by which key regulatory genes influence the function and integrity of the Drosophila male accessory gland.
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Project description:Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes. FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs
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Project description:Transposase-accessible chromatin by sequencing (ATAC-seq) has emerged as an advantageous technique to assess chromatin accessibility owing to the robustness of "tagmentation" process and a relatively faster library preparation. A comprehensive ATAC-seq protocol from Drosophila brain tissue is currently unavailable. Here, we have provided a detailed protocol of ATAC-seq assay from Drosophila brain tissue. Starting from dissection and transposition to amplification of libraries has been elaborated. Furthermore, a robust ATAC-seq analysis pipeline has been presented. The protocol can be easily adapted for other soft tissues.
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