Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array

Frédéric Biemar; David A Nix; Jessica Piel; Brant Peterson; Matthew Ronshaugen; Victor Sementchenko; Ian Bell; J Robert Manak; Michael S Levine

doi:10.1073/pnas.0604484103

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Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array

Journal article

Open access

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Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array

Frédéric Biemar, David A Nix, Jessica Piel, Brant Peterson, Matthew Ronshaugen, Victor Sementchenko, Ian Bell, J Robert Manak and Michael S Levine

Proceedings of the National Academy of Sciences - PNAS, Vol.103(34), pp.12763-12768

08/22/2006

DOI: 10.1073/pnas.0604484103

PMCID: PMC1636694

PMID: 16908844

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Abstract

Dorsal-ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence-specific transcription factor distributed in a broad nuclear gradient in the precellular embryo. Previous studies have identified as many as 70 protein-coding genes and one microRNA (miRNA) gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation. Here, we attempt to extend this analysis by identifying additional DV patterning genes using a recently developed whole-genome tiling array. This analysis led to the identification of another 30 protein-coding genes, including the Drosophila homolog of Idax, an inhibitor of Wnt signaling. In addition, remote 5' exons were identified for at least 10 of the approximately 100 protein-coding genes that were missed in earlier annotations. As many as nine intergenic uncharacterized transcription units were identified, including two that contain known microRNAs, miR-1 and -9a. We discuss the potential functions of these recently identified genes and suggest that intronic enhancers are a common feature of the DV gene network.

Drosophila melanogaster - embryology

Animals

Oligonucleotide Array Sequence Analysis

Gene Expression Regulation, Developmental

Embryo, Nonmammalian - metabolism

Genome, Insect - genetics

Embryo, Nonmammalian - embryology

Body Patterning - genetics

Drosophila melanogaster - genetics

Details

Title: Subtitle: Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array
Creators: Frédéric Biemar - Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
David A Nix
Jessica Piel
Brant Peterson
Matthew Ronshaugen
Victor Sementchenko
Ian Bell
J Robert Manak
Michael S Levine
Resource Type: Journal article
Publication Details: Proceedings of the National Academy of Sciences - PNAS, Vol.103(34), pp.12763-12768
DOI: 10.1073/pnas.0604484103
PMID: 16908844
PMCID: PMC1636694
NLM abbreviation: Proc Natl Acad Sci U S A
ISSN: 0027-8424
eISSN: 1091-6490
Publisher: United States
Grant note: N01-CO-12400 / NCI NIH HHS R37 GM046638 / NIGMS NIH HHS R01 GM046638 / NIGMS NIH HHS GM46638 / NIGMS NIH HHS N01CO12400 / NCI NIH HHS
Language: English
Date published: 08/22/2006
Academic Unit: Stead Family Department of Pediatrics; Biology; Craniofacial Anomalies Research Center
Record Identifier: 9983991960002771

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