Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos
Fig 1
Transcription dynamics in the fly embryo.
(A) The three models of transcription dynamics considered in this paper. From left to right: the two state model, the cycle model and the Gamma model (see SI Sections B, D and E). (B) Example of the promoter state dynamics (either ON or OFF) as a function of time. We assume that the polymerase is abundant and every time the promoter is ON and is not flanked by the previous polymerase a new polymerase will start transcribing. The function X(t) in black is non-zero when a polymerase is occupying the transcription initiation site and zero otherwise. (C) In the ON state, the promoter (Pr) is accessible to RNA polymerases (Pol II) that initiate the transcription of the target gene and the 24× MS2 loops. As the 24× target mRNA is elongated MCP-GFP fluorescent molecules bind a detectable fluorescence signal. (D) MCP-GFP molecules labeling several mRNAs co-localize at the transcription loci, which appear as green spots under the confocal microscope. The spot intensities are then extracted over time and classified by each nuclei’s position in the Drosophila embryo as Anterior, Boundary and Posterior. The spatial resolution of the spots is limited by the Abel limit, which is ∼ 200nm. The ability to identify spots is also limited by the background level of free MCP-GFP. Typical spot sizes are ∼ 260nm, giving an upper bound on the size of the transcription site. (E) The gene is divided into r sites of size 150 base pairs, indexed by i. The presence or absence of a polymerase at site i on the gene as a function of time is given by the promoter occupancy in B and a delay time that depends on the speed of the polymerase. (F) A cartoon representing the type of experimental signal we analyze (see S1 Fig for real traces): one spot’s intensity as a function of time, corresponding to the arrival of RNA polymerases in (E) and the promoter state in (B).