Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array
Open accessAbstract
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 ≈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.
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Tiling arrays identified specific, differentially expressed splice products (e.g., bunched) and miRNAs (mir1 and mir9a) that could not be distinguished with standard arrays containing probes designed only to assay predicted gene products.
“the tiling arrays also identified specific, differentially expressed splice products (e.g., bunched) and miRNAs (mir1 and mir9a), that could not be distinguished with standard arrays containing probes designed only to assay predicted gene products.”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Biemar et al. 2006
Tiling arrays increased the number of genes exhibiting Dorsal-dependent regulation from approximately 50 predicted by standard chip hybridizations to approximately 100.
“Besides increasing the number of genes exhibiting Dorsal-dependent regulation from approximately 50 predicted by standard chip hybridizations (Stathopoulos et al. 2002) to approximately 100 (Biemar et al. 2006)”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Biemar et al. 2006
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- Authors
- Biemar, F., Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., Manak, J. R., & Levine, M. S.
- Affiliations
- University of California, Berkeley (US)
- Affymetrix (United States) (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2006-08-22
- Volume
- 103
- Issue
- 34
- Pages
- 12763-12768
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1636694
- OpenAlex
- W2164146453
- Cited by
- 53
- References
- 45
- Citations by year
- 2025: 1 · 2024: 2 · 2023: 1 · 2022: 1 · 2021: 1 · 2019: 2 · 2017: 2 · 2016: 3 · 2015: 3 · 2014: 4 · 2013: 2 · 2012: 3
- FWCI
- 2.99
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Funders
- National Institutes of Health (n01co12400-79-0-22)
- National Cancer Institute (N01CO12400, N01-CO-012400)
- National Institute of General Medical Sciences (R37GM046638, GM-46638, R01GM046638)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- gene regulatory networks, gastrulation, Wnt signaling inhibition, microRNA genes, miR-1, intronic enhancer
- MeSH terms
- Animals, Drosophila melanogaster, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Body Patterning, Oligonucleotide Array Sequence Analysis, Genome, Insect
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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