title: Accurate measurements of dynamics and reproducibility in small genetic networks.
abstract: Quantification of gene expression has become a central tool for understanding genetic networks. In many systems, the only viable way to measure protein levels is by immunofluorescence, which is notorious for its limited accuracy. Using the early Drosophila embryo as an example, we show that careful identification and control of experimental error allows for highly accurate gene expression measurements. We generated antibodies in different host species, allowing for simultaneous staining of four Drosophila gap genes in individual embryos. Careful error analysis of hundreds of expression profiles reveals that less than ∼20% of the observed embryo-to-embryo fluctuations stem from experimental error. These measurements make it possible to extract not only very accurate mean gene expression profiles but also their naturally occurring fluctuations of biological origin and corresponding cross-correlations. We use this analysis to extract gap gene profile dynamics with ∼1 min accuracy. The combination of these new measurements and analysis techniques reveals a twofold increase in profile reproducibility owing to a collective network dynamics that relays positional accuracy from the maternal gradients to the pair-rule genes.
authors: Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA.
authors: Julien O
authors: JO
authors: Dubuis
authors: Reba
authors: R
authors: Samanta
authors: Thomas
authors: T
authors: Gregor
mesh_terms: D000818:Animals; D004268:DNA-Binding Proteins / Q000235:genetics / Q000276:immunology; D004330:Drosophila / Q000196:embryology / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics / Q000276:immunology; D004625:Embryo, Nonmammalian; D005455:Fluorescent Antibody Technique; D020690:GTPase-Activating Proteins / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D007091:Image Processing, Computer-Assisted; D051741:Kruppel-Like Transcription Factors / Q000235:genetics / Q000276:immunology; D012097:Repressor Proteins / Q000235:genetics / Q000276:immunology; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics / Q000276:immunology
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D020690:GTPase-Activating Proteins; C497244:Kr protein, Drosophila; D051741:Kruppel-Like Transcription Factors; D012097:Repressor Proteins; D014157:Transcription Factors; C118475:gt protein, Drosophila; C061245:hb protein, Drosophila; C074089:kni protein, Drosophila