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Development. 2019 Mar 28;146(6). pii: dev175265. doi: 10.1242/dev.175265.

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

Author information

1
Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany ali.mccorkindale@inventia.life robert.zinzen@mdc-berlin.de.
2
Biofrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
3
Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany.
4
MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA.
5
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
6
Laboratory for Bioinformatics of RNA Structure and Transcriptome Regulation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany.
7
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
8
Dana Farber Cancer Institute, Boston, MA 02215, USA.
9
Freie Universität, Institute of Biochemistry, Department of Biology, Chemistry, Pharmacy, Thielallee 63, Berlin 14195, Germany.

Abstract

Cell type specification during early nervous system development in Drosophila melanogaster requires precise regulation of gene expression in time and space. Resolving the programs driving neurogenesis has been a major challenge owing to the complexity and rapidity with which distinct cell populations arise. To resolve the cell type-specific gene expression dynamics in early nervous system development, we have sequenced the transcriptomes of purified neurogenic cell types across consecutive time points covering crucial events in neurogenesis. The resulting gene expression atlas comprises a detailed resource of global transcriptome dynamics that permits systematic analysis of how cells in the nervous system acquire distinct fates. We resolve known gene expression dynamics and uncover novel expression signatures for hundreds of genes among diverse neurogenic cell types, most of which remain unstudied. We also identified a set of conserved long noncoding RNAs (lncRNAs) that are regulated in a tissue-specific manner and exhibit spatiotemporal expression during neurogenesis with exquisite specificity. lncRNA expression is highly dynamic and demarcates specific subpopulations within neurogenic cell types. Our spatiotemporal transcriptome atlas provides a comprehensive resource for investigating the function of coding genes and noncoding RNAs during crucial stages of early neurogenesis.

KEYWORDS:

Drosophila melanogaster; Embryogenesis; Neurogenesis; Spatiotemporal transcriptome; lncRNA

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