PMID:21693522

Citation	Schroeder, MD, Greer, C and Gaul, U (2011) How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation. Development 138:3067-78
Abstract	The generation of metameric body plans is a key process in development. In Drosophila segmentation, periodicity is established rapidly through the complex transcriptional regulation of the pair-rule genes. The 'primary' pair-rule genes generate their 7-stripe expression through stripe-specific cis-regulatory elements controlled by the preceding non-periodic maternal and gap gene patterns, whereas 'secondary' pair-rule genes are thought to rely on 7-stripe elements that read off the already periodic primary pair-rule patterns. Using a combination of computational and experimental approaches, we have conducted a comprehensive systems-level examination of the regulatory architecture underlying pair-rule stripe formation. We find that runt (run), fushi tarazu (ftz) and odd skipped (odd) establish most of their pattern through stripe-specific elements, arguing for a reclassification of ftz and odd as primary pair-rule genes. In the case of run, we observe long-range cis-regulation across multiple intervening genes. The 7-stripe elements of run, ftz and odd are active concurrently with the stripe-specific elements, indicating that maternal/gap-mediated control and pair-rule gene cross-regulation are closely integrated. Stripe-specific elements fall into three distinct classes based on their principal repressive gap factor input; stripe positions along the gap gradients correlate with the strength of predicted input. The prevalence of cis-elements that generate two stripes and their genomic organization suggest that single-stripe elements arose by splitting and subfunctionalization of ancestral dual-stripe elements. Overall, our study provides a greatly improved understanding of how periodic patterns are established in the Drosophila embryo.
Links	PubMed PMC3119311 Online version:10.1242/dev.062141
Keywords	Animals; Animals, Genetically Modified; Body Patterning/physiology; DNA-Binding Proteins/metabolism; Drosophila/embryology; Drosophila Proteins/metabolism; Embryo, Nonmammalian/anatomy & histology; Embryo, Nonmammalian/embryology; Fushi Tarazu Transcription Factors/metabolism; Gene Expression Regulation, Developmental/physiology; Genotype; Homeodomain Proteins/metabolism; In Situ Hybridization; Nuclear Proteins/metabolism; Periodicity; Transcription Factors/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
DROME:ODD	involved_in	GO:0007389: pattern specification process	ECO:0000315: mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
DROME:ODD		GO:0007389: pattern specification process	ECO:0000315:		P		See Figure 5: "observed clear defects in pair-rule gene expression patterns in slp and prd mutants"	complete CACAO 3718

References

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