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Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

ABSTRACT: Understanding transcriptional regulatory networks requires the identification and characterization of cis-regulatory modules (CRMs), DNA sequences which can direct expression of associated genes to a specific cell type and/or developmental stage. Reporter assays for the capacity of a candidate CRM to activate a heterologous promoter have been productive but suffer limited throughput or fail to convey information on cell type specificity. We have developed an assay in which reporter constructs containing a pool of candidate CRMs are introduced in parallel to Drosophila embryos along with a common cell-type-specific second marker; candidate CRMs isolated by PCR from FACS-purified double-positive cells can by quantitated by high-throughput sequencing, and their relative abundance compared to those in the input cell population to detect activity in the cell type (or types) of interest.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE41503 | GEO | 2013/07/13

SECONDARY ACCESSION(S): PRJNA177318

REPOSITORIES: GEO

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Project description:The abstract of the manuscript titled "Identification of co-regulated genes and cis-regulatory modules in Drosophila contractile cardiomyocytes" is given below: "Understanding how sets of genes are co-regulated to generate cell diversity during metazoan development is a major challenge. This requires the identification of tightly co-expressed genes in a given developmental process, of the responsible cis-regulatory modules, and of the combination of trans-acting transcription factors. We chose the Drosophila cardiac tube to address this issue. The cardiac tube is composed of a rostral aorta and a caudal heart, with distinct morphologies and functions and its development is controlled by conserved transcription factors. Our goal was to identify heart specific expressed genes and to use a combination of genetic and bioinformatic tools to identify and characterize their heart cis-regulatory modules (CRMs). By combined candidate gene approach and microarray experiments, we found 15 different genes that are specifically co-expressed in the contractile cardiomyocytes of the heart. Potential heart-specific CRMs were retrieved from evolutionary conserved non-coding sequences that were ranked according to an integrated score based on combinations of conserved occurrences of potential binding sites for transcription factors known to be expressed in the cardiovascular system, namely Abd-A, Tin, GATA, Mef2, Hand, and T-box factors. Candidate CRMs were then tested in vivo by generating nGFP reporter construct transgenic flies, allowing the identification of three heart enhancers precisely reproducing endogenous gene expression in the heart. We identified 15 genes that are tightly co-regulated in the contractile cardiomyocytes of the heart and for three of them found the responsible enhancer through computational predictions. A computational post-analysis suggests that different combinations of heart transcription factors may regulate these enhancers and permits to further refine the in silico identification of heart-specific CRMs."

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Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

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