Systematic determination of patterns of gene expression during Drosophila embryogenesis

BackgroundCell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription.ResultsAs a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, we examined 2,179 genes by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos. The photomicrographs were annotated using controlled vocabularies for anatomical structures that are organized into a developmental hierarchy. We also generated a detailed time course of gene expression during embryogenesis using microarrays to provide an independent corroboration of the in situ hybridization results. All image, annotation and microarray data are stored in publicly available database. We found that the RNA transcripts of about 1% of genes show clear subcellular localization. Nearly all the annotated expression patterns are distinct. We present an approach for organizing the data by hierarchical clustering of annotation terms that allows us to group tissues that express similar sets of genes as well as genes displaying similar expression patterns.ConclusionsAnalyzing gene-expression patterns by in situ hybridization to whole-mount embryos provides an extremely rich dataset that can be used to identify genes involved in developmental processes that have been missed by traditional genetic analysis. Systematic analysis of rigorously annotated patterns of gene expression will complement and extend the types of analyses carried out using expression microarrays.

[1]  P. Harrison,et al.  Localisation of cellular globin messenger RNA by in situ hybridisation to complementary DNA , 1973, FEBS letters.

[2]  M. Bownes,et al.  A photographic study of development in the living embryo of Drosophila melanogaster. , 1975, Journal of embryology and experimental morphology.

[3]  C. Nüsslein-Volhard,et al.  Mutations affecting segment number and polarity in Drosophila , 1980, Nature.

[4]  Stephen T. Crews,et al.  The Drosophila single-minded gene encodes a nuclear protein with sequence similarity to the per gene product , 1988, Cell.

[5]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[6]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[7]  Prof. Dr. José A. Campos-Ortega,et al.  The Embryonic Development of Drosophila melanogaster , 1997, Springer Berlin Heidelberg.

[8]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[9]  Martin Vingron,et al.  Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning , 1998, Mechanisms of Development.

[10]  S. Lewis,et al.  A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. J. Schroeder,et al.  The FlyBase database of the Drosophila Genome Projects and community literature. , 2002, Nucleic acids research.

[12]  D. Botstein,et al.  Exploring the new world of the genome with DNA microarrays , 1999, Nature Genetics.

[13]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[15]  H. Lehrach,et al.  Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos , 2000, Mechanisms of Development.

[16]  M Vingron,et al.  In silico analysis of gene expression patterns during early development of Xenopus laevis. , 2000, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[17]  G M Rubin,et al.  A Drosophila complementary DNA resource. , 2000, Science.

[18]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[19]  J. Wittbrodt,et al.  An in situ hybridization screen for the rapid isolation of differentially expressed genes , 2000, Development Genes and Evolution.

[20]  E. Chudin,et al.  Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip® arrays , 2001, Genome Biology.

[21]  K. White,et al.  Patterns of Gene Expression During Drosophila Mesoderm Development , 2001, Science.

[22]  Cheng Li,et al.  Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application , 2001, Genome Biology.

[23]  Expression profiling by systematic high-throughput in situ hybridization to whole-mount embryos. , 2001, Methods in molecular biology.

[24]  Joshua M. Stuart,et al.  A Gene Expression Map for Caenorhabditis elegans , 2001, Science.

[25]  B. S. Baker,et al.  Gene Expression During the Life Cycle of Drosophila melanogaster , 2002, Science.

[26]  R. Weiss,et al.  Profiling patterned transcripts in Drosophila embryos. , 2002, Genome research.

[27]  S. Lewis,et al.  An integrated computational pipeline and database to support whole-genome sequence annotation , 2002, Genome Biology.

[28]  Piero Carninci,et al.  The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. , 2002, Genome research.

[29]  G. Rubin,et al.  A Drosophila full-length cDNA resource , 2002, Genome Biology.

[30]  The FlyBase database of the Drosophila genome projects and community literature. , 2003, Nucleic acids research.

[31]  F. W. Robertson,et al.  Localisation of reiterated nucleotide sequences in Drosophila and mouse by in situ hybridisation of complementary RNA , 2004, Chromosoma.

[32]  D. Tautz,et al.  A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback , 1989, Chromosoma.