title: Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
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.
authors.affiliation: Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Hooper
authors.forename: Stephanie
authors.initials: S
authors.lastname: Boué
authors.forename: Roland
authors.initials: R
authors.lastname: Krause
authors.forename: Lars J
authors.initials: LJ
authors.lastname: Jensen
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
authors.forename: Murad
authors.initials: M
authors.lastname: Ghanim
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
authors.forename: Eileen E M
authors.initials: EE
authors.lastname: Furlong
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000704:Analysis of Variance; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D047108:Embryonic Development / Q000235:genetics*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D017403:In Situ Hybridization; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D050809:POU Domain Factors / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D051880:Receptors, Notch / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; C497759:N protein, Drosophila; D050809:POU Domain Factors; D012333:RNA, Messenger; D051880:Receptors, Notch; D014157:Transcription Factors; C064045:delta protein; C072851:pdm2 protein, Drosophila; C402787:wor protein, Drosophila