Dynamic expression of pleiotropic developmental genes during Drosophila embryogenesis

Abstract

During embryonic development transcription must be precisely regulated over space and time to differentiate tissues and form organs. Organogenesis is directed by a set of pleiotropic transcription factors that are conserved across species and are expressed in diverse tissues during embryogenesis. These transcription factors drive spatiotemporal patterns of gene expression by binding to regulatory DNA called enhancers. Distinct enhancers are thought to drive expression in each tissue. The field has made enormous progress on understanding how enhancers limit expression to a specific tissue, but much less is understood about how enhancers control the dynamics of gene expression. These dynamics can vary widely between developing tissues as genes may be expressed for minutes to days and precise timescales are critical for both cell differentiation and tissue function. In this work, we investigate how the developmental gene even-skipped (eve) is quantitatively expressed during multiple stages of embryogenesis in Drosophila melanogaster, using in vivo microscopy of nascent transcription from the endogenous eve locus. This method allows us to compare the detailed dynamics of eve expression in diverse tissues. We demonstrate that the dynamics of eve transcription are quantitatively similar between tissues, despite expression being controlled by different enhancers and expression continuing over different timescales. Further, we examine the transcription factor binding site composition of eve’s tissue-specific enhancers to probe how these enhancers may contribute to tissue specification in diverse contexts. Our results provide quantitative insights into gene regulation in multiple tissues in the endogenous context during development, a context that has traditionally been difficult to probe. Our results suggest that different timescales of gene expression can be achieved using the same underlying dynamics of transcription and therefore challenges existing conceptions of enhancer-driven transcriptional regulation. This underscores the need to further probe how different timescales of expression are achieved through additional mechanisms of gene regulation. Together, this work provides new insight into how conserved and critical developmental genes can be re-used during embryogenesis.