Precision of readout at the hunchback gene: analyzing short transcription time traces in living fly embryos

TL;DR

This study develops a novel autocorrelation analysis method to quantify transcription dynamics from short live imaging traces of the hunchback gene in fly embryos, revealing bursty transcription and limited positional precision.

Contribution

It introduces a tailored autocorrelation approach to analyze short transcription traces and uncovers signatures of bursty transcription initiation in live embryo data.

Findings

Transcription traces are too short for traditional analysis methods.

Bursty transcription initiation signatures are identified.

Positional precision of hunchback expression is limited at early cycles.

Abstract

The simultaneous expression of the hunchback gene in the numerous nuclei of the developing fly embryo gives us a unique opportunity to study how transcription is regulated in living organisms. A recently developed MS2-MCP technique for imaging nascent messenger RNA in living Drosophila embryos allows us to quantify the dynamics of the developmental transcription process. The initial measurement of the morphogens by the hunchback promoter takes place during very short cell cycles, not only giving each nucleus little time for a precise readout, but also resulting in short time traces of transcription. Additionally, the relationship between the measured signal and the promoter state depends on the molecular design of the reporting probe. We develop an analysis approach based on tailor made autocorrelation functions that overcomes the short trace problems and quantifies the dynamics of transcription initiation. Based on live imaging data, we identify signatures of bursty transcription initiation from the hunchback promoter. We show that the precision of the expression of the hunchback gene to measure its position along the anterior-posterior axis is low both at the boundary and in the anterior even at cycle 13, suggesting additional post-transcriptional averaging mechanisms to provide the precision observed in fixed embryos.