A Multiscale Investigation of Bicoid-Dependent Transcriptional Events in Drosophila Embryos

Abstract

BackgroundMorphogen molecules form concentration gradients to provide spatial information to cells in a developing embryo. Precisely how cells decode such information to form patterns with sharp boundaries remains an open question. For example, it remains controversial whether the Drosophila morphogenetic protein Bicoid (Bcd) plays a transient or sustained role in activating its target genes to establish sharp expression boundaries during development.Methodology/Principal FindingsIn this study, we describe a method to simultaneously detect Bcd and the nascent transcripts of its target genes in developing embryos. This method allows us to investigate the relationship between Bcd and the transcriptional status of individual copies of its target genes on distinct scales. We show that, on three scales analyzed concurrently—embryonic, nuclear and local, the actively-transcribing gene copies are associated with high Bcd concentrations. These results underscore the importance of Bcd as a sustained input for transcriptional decisions of individual copies of its target genes during development. We also show that the Bcd-dependent transcriptional decisions have a significantly higher noise than Bcd-dependent gene products, suggesting that, consistent with theoretical studies, time and/or space averaging reduces the noise of Bcd-activated transcriptional output. Finally, our analysis of an X-linked Bcd target gene reveals that Bcd-dependent transcription bursts at twice the frequency in males as in females, providing a mechanism for dosage compensation in early Drosophila embryos.Conclusion/SignificanceOur study represents a first experimental uncovering of the actions of Bcd in controlling the actual transcriptional events while its positional information is decoded during development. It establishes a sustained role of Bcd in transcriptional decisions of individual copies of its target genes to generate sharp expression boundaries. It also provides an experimental evaluation of the effect of time and/or space averaging on Bcd-dependent transcriptional output, and establishes a dosage compensation mechanism in early Drosophila embryos.

Scaling of the Bicoid morphogen gradient by a volume-dependent production rate

“…How a Bcd concentration gradient is formed remains highly controversial (Coppey et al, 2007;Deng et al, 2010;Gregor et al, 2008;Gregor et al, 2007b;Grimm and Wieschaus, 2010;Little et al, 2011;Porcher et al, 2010;Spirov et al, 2009), even whether the positional information provided by Bcd is decoded before the gradient reaches its steady state (Bergmann et al, 2007;Bergmann et al, 2008;Bialek et al, 2008;de Lachapelle and Bergmann, 2010a;de Lachapelle and Bergmann, 2010b;He et al, 2011;Jaeger, 2010;. Although we have not specifically investigated the process of Bcd gradient formation, the observed scaling properties of the Bcd gradient may be readily explained by a diffusion model if the Bcd production rate is scaled with embryo volume (Deng et al, 2010).…”

“…a volumedependent Bcd production rate, represents an early-acting scaling mechanism along the A-P axis in D. melanogaster embryos. In addition, since Bcd acts as a direct and sustained input for target gene transcription (He et al, 2010a;He et al, 2010b;He et al, 2008;He et al, 2011;, the scaling properties of the Bcd gradient also represent a critical means by which scaled A-P patterning is achieved in broad regions of the embryo (see below for further discussion).…”

Morphogen gradient formation and action

“…Exactly how the positional information provided by the Bcd gradient feeds into precise patterning decisions is a subject of intense theoretical investigations. 34,35,[37][38][39] In a recent experimental study, 40 we investigated the role of Bcd in the actual transcriptional events of its target genes in developing embryos. Our results suggest that Bcd acts as a direct and sustained input for these transcriptional events.…”

“…In addition, a comparison between the noise in Bcd-dependent transcriptional events and the noise in Bcd-dependent transcriptional products provides a first experimental demonstration of the effect of time/space averaging in reducing the output noise. 40 useful framework in guiding our thinking and analyses of the Bcd gradient formation process.…”

Transcriptional activators and activation mechanisms

“…Recent studies of evaluating the transcriptional products of individual cells suggest that transcription takes place as discrete bursts (Elowitz et al, 2002;Kaern et al, 2005;Raser and O'Shea, 2005;Golding and Cox, 2006;Pare et al, 2009;Chubb and Liverpool, 2010;To and Maheshri, 2010). Transcriptional activators appear to increase the frequency or probability of such bursts, as opposed to the number of transcripts produced per burst To and Maheshri, 2010;He et al, 2011).…”