Dynamics of Drosophila endoderm specification

Abstract

Significance To understand developmental patterning of an organism, it is necessary to accurately measure how the state of a gene regulatory network is changing over time. One way of extracting dynamics of a network involves simultaneously imaging several reporters within fixed tissue. Reconstructing dynamics from such data requires staging many samples over time and often leads to low temporal resolution. Time-lapse microscopy of fluorescent transcriptional reporters has revolutionized studies of biological dynamics at the single-cell level. However, this method is limited by the number of reporters that can be imaged at one time. We present a computational method for addressing this problem and demonstrate its application by modeling the gene regulatory network underlying Drosophila posterior patterning and reconstructing its developmental dynamics.

A timer gene network is spatially regulated by the terminal system in theDrosophilaembryo

“…Most (11/18) of these proposed interactions originate from this study, although we also find support for previously proposed interactions related to the patterning of tll , hkb , fkh and wg (Figure 8B). (For a recent quantitative model of posterior gut specification using a network similar to Figure 8B, see Keenan et al, 2022. )…”

Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the earlyDrosophilaembryo

“…We varied the intensity of the blue light dose to identify intensities that would produce byn responses similar to those endogenous responses observed by Keenan et al (2022). Under a high-intensity blue light dose (“high light”), byn was expressed in a transient pulse, with MCP-labeled transcriptional foci detected for only 10-15 min after the start of NC14 ( Figure 1D , top, Movie S1 ).…”

“…Prior studies have shown that posterior byn expression is dynamic and forms two different domains (Kispert et al 1994; Keenan et al 2022). At the posterior pole, byn expression occurs in a transient pulse at the beginning of nuclear cycle 14 (NC14), whereas at more interior positions, byn is sustained longer into NC14 ( Figure 1B ).…”

“…We generated Drosophila embryos that expressed the OptoSOS system for Ras/ERK pathway activation (Johnson et al 2017; Toettcher et al 2013) and a fluorescent MCP protein for visualizing transcription of MS2-tagged transcripts (Garcia et al 2013). These OptoSOS/MCP embryos also contained MS2 stem loops in the endogenous byn 5’UTR ( byn -MS2) (Keenan et al 2022). To avoid overlap with the endogenous terminal system, we stimulated a region on the embryo’s ventral surface that is sufficiently far from the pole to lack byn , tll , or hkb transcription when embryos are grown in the dark, but where tll , hkb , and byn expression could be readily induced by optogenetic stimulation ( Figure S1 ).…”

“…First, the pattern of byn expression is dynamic: it is initially expressed as a cap covering the entire posterior domain, only resolving into a stripe in late nuclear cycle 14 (NC14) ( Figure 1B ) (Kispert et al 1994). Recently, Keenan et al (2022) showed that these dynamics derive from changes in byn transcription: there is a domain of transient byn transcription at the pole and a domain of sustained byn transcription at interior positions. The source of these byn dynamics is not known, nor is it clear how byn might be expressed in the same posterior domain as its negative regulator hkb .…”