Proper development of the adult fly relies on the correct spatial assignment of cell types during fly development. The different identities of cells are determined by sequentially expressing particular subsets of genes in different parts of the embryo.
Bicoid activated Hunchback is essential for Antero-Posterior patterning (among others).
The precision of the timing and spatial expression of the hunchback gene is regulated at the level of gene expression. This process involves the assembly of the transcription machinery and depends on the concentrations of the maternal gradients.
Using recent live imaging experiments that span several cell cycles we can access information on the dynamics of transcription initiation and gain insight into the dynamics of transcription.
We develop an analysis approach based on a tailor made time dependent autocorrelation function that overcomes all experimental and computational problems to quantify the dynamics of transcription initiation. Both eukaryotic and prokaryotic transcription can involve more than just switching between an active and inactive state, so we extend our analysis to increasing complexity that allows us to infer the effective number of transcription initiation steps and the rates for progressing through them.
We first discuss the accuracy and potential of our method on simulated data and then analyse live MS2-MCP traces from developing fruit fly embryos. We identify the bursty nature of transcription initiation from the hunchback promoter. We show that in the anterior region where Bicoid levels saturate the promoter transcription dynamics is extremely reproducible from cell cycle 11 to 13. We give a new method for computing the limiting accuracy of the antero-posterior boundary sharpness using only the parameters of our model.