title: A combinatorial code for pattern formation in Drosophila oogenesis.
abstract: Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.
authors.affiliation: Lewis-Sigler Institute for Integrative Genomics and Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: Yakoby
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Bristow
authors.forename: Danielle
authors.initials: D
authors.lastname: Gong
authors.forename: Xenia
authors.initials: X
authors.lastname: Schafer
authors.forename: Jessica
authors.initials: J
authors.lastname: Lembong
authors.forename: Jeremiah J
authors.initials: JJ
authors.lastname: Zartman
authors.forename: Marc S
authors.initials: MS
authors.lastname: Halfon
authors.forename: Trudi
authors.initials: T
authors.lastname: Schüpbach
authors.forename: Stanislav Y
authors.initials: SY
authors.lastname: Shvartsman
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000196:embryology / Q000502:physiology*; D004848:Epithelium / Q000378:metabolism; D005260:Female; D018507:Gene Expression Regulation, Developmental; D009866:Oogenesis; D006080:Ovarian Follicle / Q000378:metabolism