Identification of Tightly Regulated Groups of Genes During Drosophila Melanogaster Embryogenesis

Mol Syst Biol. 2007;3:72. doi: 10.1038/msb4100112. Epub 2007 Jan 16.

Abstract

Time-series analysis of whole-genome expression data during Drosophila melanogaster development indicates that up to 86% of its genes change their relative transcript level during embryogenesis. By applying conservative filtering criteria and requiring 'sharp' transcript changes, we identified 1534 maternal genes, 792 transient zygotic genes, and 1053 genes whose transcript levels increase during embryogenesis. Each of these three categories is dominated by groups of genes where all transcript levels increase and/or decrease at similar times, suggesting a common mode of regulation. For example, 34% of the transiently expressed genes fall into three groups, with increased transcript levels between 2.5-12, 11-20, and 15-20 h of development, respectively. We highlight common and distinctive functional features of these expression groups and identify a coupling between downregulation of transcript levels and targeted protein degradation. By mapping the groups to the protein network, we also predict and experimentally confirm new functional associations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Analysis of Variance
  • Animals
  • Cluster Analysis
  • Computational Biology
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / embryology
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / metabolism
  • Embryonic Development / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Gene Regulatory Networks
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • In Situ Hybridization
  • Intracellular Signaling Peptides and Proteins
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Oligonucleotide Array Sequence Analysis
  • POU Domain Factors / genetics
  • POU Domain Factors / metabolism
  • RNA, Messenger / metabolism
  • Receptors, Notch / genetics
  • Receptors, Notch / metabolism
  • Reproducibility of Results
  • Time Factors
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic*

Substances

  • Drosophila Proteins
  • Homeodomain Proteins
  • Intracellular Signaling Peptides and Proteins
  • Membrane Proteins
  • N protein, Drosophila
  • POU Domain Factors
  • RNA, Messenger
  • Receptors, Notch
  • Transcription Factors
  • delta protein
  • pdm2 protein, Drosophila
  • wor protein, Drosophila