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Targeted DamID-seq of the Drosophila carpet glia

ABSTRACT: Targeted DamID-seq of the Drosophila carpet glia

PROVIDER: PRJEB30096 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2983380.fastq.gz	Fastqsanger.gz
	ERR2983390.fastq.gz	Fastqsanger.gz
	ERR2983400.fastq.gz	Fastqsanger.gz
	ERR2983410.fastq.gz	Fastqsanger.gz
	ERR2983420.fastq.gz	Fastqsanger.gz

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Targeted DamID-seq of the Drosophila carpet glia

Project description:Identification of POLII binding to profile the expressed genes in the carpet glia

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Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. We determined DamID scores for Polycomb, normalized by Dam only control, for Drosophila larval central brain, larval fat bodies and repo+ glial cells of larval central brain. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.

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Project description:kdm5 is an essential gene in Drosophila that has critical developmental roles in the prothoracic gland cells of the larval ring gland. To profile KDM5 binding within these cells and this developmental stage, we performed Targeted DamID (TaDa). By profiling the nearest genes to significant TaDa peaks (FDR < 0.01), we identified 5815 candidate KDM5 target genes. Interestingly, 42% of these candidate KDM5 target genes appear to be conserved across multiple cellular contexts in Drosophila and span many cellular processes for future investigation.

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Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. RNA sequencing of 3 samples, each using 2 biological replicates.

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Project description:This project’s aim was to compare the transcriptional profiles of olfactory sensory neurons in Drosophila melanogaster in order to identify novel genes that specify neuron-specific functions/phenotypes or may otherwise be involved in the development of the olfactory system. The isolation of sufficient numbers of intact olfactory sensory neurons (OSN) from the antenna of Drosophila melanogaster has so far limited single-cell transcriptomic approaches being applied to the adult fly antenna. Targeted DamID (TaDa) provides an alternative approach for profiling transcriptional activity in a cell-specific manor that bypasses the need for isolating OSN. Using the Gal4/UAS system, we applied TaDa to seven OSN populations and compared differences in Pol II occupancy for genes across these datasets.

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Project description:Tissue homeostasis relies on stem cell activity which drives replacement of differentiated cells to maintain tissue integrity and function. The stress-inducible transcription factor Ets21c promotes tissue renewal in the Drosophila adult intestine by controlling intestinal stem cell proliferation and apoptosis of mature enterocytes. To determine how Ets21c fulfills these distinct tasks in the different cell types of the gut, we exploited a genome-wide in vivo Targeted DamID mapping approach to identify its putative direct targets. In young unstressed midguts, Ets21c contacts regulatory loci occupied by as well as devoid of the Polymerase II binding. Follow-up functional genetic studies in intestinal stem cells and enterocytes demonstrate that Ets21c controls cell type-specific sets of target genes that orchestrate cellular behavior via intrinsic and non-autonomous signaling mechanisms. Ets21c thus emerges as a vital determinant of adult health and lifespan.

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