Dataset Information

A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.

ABSTRACT: Here, we describe the embryonic central nervous system expression of 5,000 GAL4 lines made using molecularly defined cis-regulatory DNA inserted into a single attP genomic location. We document and annotate the patterns in early embryos when neurogenesis is at its peak, and in older embryos where there is maximal neuronal diversity and the first neural circuits are established. We note expression in other tissues, such as the lateral body wall (muscle, sensory neurons, and trachea) and viscera. Companion papers report on the adult brain and larval imaginal discs, and the integrated data sets are available online (http://www.janelia.org/gal4-gen1). This collection of embryonically expressed GAL4 lines will be valuable for determining neuronal morphology and function. The 1,862 lines expressed in small subsets of neurons (<20/segment) will be especially valuable for characterizing interneuronal diversity and function, because although interneurons comprise the majority of all central nervous system neurons, their gene expression profile and function remain virtually unexplored.

SUBMITTER: Manning L

PROVIDER: S-EPMC3523218 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.

Manning Laurina L Heckscher Ellie S ES Purice Maria D MD Roberts Jourdain J Bennett Alysha L AL Kroll Jason R JR Pollard Jill L JL Strader Marie E ME Lupton Josh R JR Dyukareva Anna V AV Doan Phuong Nam PN Bauer David M DM Wilbur Allison N AN Tanner Stephanie S Kelly Jimmy J JJ Lai Sen-Lin SL Tran Khoa D KD Kohwi Minoree M Laverty Todd R TR Pearson Joseph C JC Crews Stephen T ST Rubin Gerald M GM Doe Chris Q CQ

Cell reports 20121011 4

Here, we describe the embryonic central nervous system expression of 5,000 GAL4 lines made using molecularly defined cis-regulatory DNA inserted into a single attP genomic location. We document and annotate the patterns in early embryos when neurogenesis is at its peak, and in older embryos where there is maximal neuronal diversity and the first neural circuits are established. We note expression in other tissues, such as the lateral body wall (muscle, sensory neurons, and trachea) and viscera. ...[more]

PMID: 23063363

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Project description:BackgroundCis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs.DescriptionIt is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality.ConclusionscisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable hypotheses for the molecular mechanisms of metazoan gene regulation. We believe that the information deposited in cisMEP will greatly facilitate the comparative usage of different CRM prediction tools and will help biologists to study the modular regulatory mechanisms between different TFs and their target genes.

Dataset Information

A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.

Publications

A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.

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