Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription

Abstract

For over 40 years, the Bicoid-hunchback (Bcd-hb) system in the fruit fly embryo has been used as a model to study how positional information in morphogen concentration gradients is robustly translated into step-like responses. A body of quantitative comparisons between theory and experiment have since questioned the initial paradigm that the sharp hb transcription pattern emerges solely from diffusive biochemical interactions between the Bicoid transcription factor and the gene promoter region. Several alternative mechanisms have been proposed, such as additional sources of positional information, positive feedback from Hb proteins or out-of-equilibrium transcription activation. By using the MS2-MCP RNA-tagging system and analysing in real time, the transcription dynamics of synthetic reporters for Bicoid and/or its two partners Zelda and Hunchback, we show that all the early hb expression pattern features and temporal dynamics are compatible with an equilibrium model with a short decay length Bicoid activity gradient as a sole source of positional information. Meanwhile, Bicoid’s partners speed-up the process by different means: Zelda lowers the Bicoid concentration threshold required for transcriptional activation while Hunchback reduces burstiness and increases the polymerase firing rate.

A quantum walk model of Bicoid morphogen formation and interpretation

“…To circumvent this problem, the idea of spatial averaging by the nuclei was introduced in order to increase the precision to the desired level [13]. Over the years the mechanism of Gregor et al has been widely applied [13][14][15][16][17][18][19] but the problem of interpretation of BCD gradient by its primary target gene hb still remains poorly understood [19][20][21][22][23][24][25]. In fact a recent theoretical analysis has shown that spatial averaging is a priori dispensable but the treatment given is unwieldy and introduces another adhoc hypothesis of dynamically changing time windows [23].…”

“…Theories employing detailed balance arguments have also not proven much helpful in this regard [22]. Recent theoretical treatments invoking hypotheses like dynamically changing time windows predict an interpretation time of less than a minute and remain unsubstantiated in vivo [9,[23][24][25]. However, experimentally BCD is known to bind to chromatin sites in a highly transient manner, with specific binding events lasting on the order of a second, in all portions of the embryo [20].…”

“…A P ∼ 500 µm In this Letter we present what may be considered as the most straightforward and simplest solution to this perplexing problem on a proof-of-concept basis. We would like to mention at the outset that our model is fundamentally very different from the usual microscopic biased diffusion approaches employing various Markovian kinetic schemes [8] or approximate continuum models derived via rigorous homogenization procedures [27], but its real power lies in that, in addition to bringing out the fundamental limitations of conventional approaches, it can successfully explain some of the most important and elusive features of the BCD-hb system that are currently a matter of intense experimental investigation [19][20][21][22][23][24][25][26]. The treatment to be presented here should, of course, be regarded as a starting point from which to proceed to more rigorous theories.…”

Regulating the timing of enhancer transitions is key to defining sharp boundaries of Fushi tarazu expression in the Drosophila embryo

“…Modelling how repressors specify the edge of Ftz stripes may provide a unique opportunity to extend the well-developed theoretical frameworks that connect enhancer sequence to boundary specification by activator proteins. The best-known examples of such studies are predictions for how the Bicoid activator gradient specifies the Hunchback boundary [38][39][40][41][42] . Compared to Hunchback, the Ftz boundaries are specified much faster and are much sharper, which will pose new challenges to existing models that would likely yield fundamentally new insights.…”

Revisitingbicoidfunction: complete inactivation reveals an additional fundamental role inDrosophilaegg geometry specification

“…The resulting bcd mutant faithfully recapitulated the appearance of the strongest bcd alleles (Huang et al, 2017). In a recent study (Fernandes et al, 2022), a complete removal of the bcd locus based on CRISPR technology was achieved. However, no in-depth analysis was conducted using this allele.…”