Spatial Ratiometric Analysis for Intrinsic Plant Promoter Activity

Rational design of synthetic gene networks requires accurate characterisation of the genetic elements controlling them. In eukaryotic multicellular systems, gene activity can either be restricted spatially to particular tissues or have ubiquitous expression, a trait which is in part controlled by the promoter which drives that gene. Furthermore, transcriptional activity can be affected by the genetic context in which the circuit is located as well as by extrinsic factors such as metabolic state.

Here we present a method for studying promoter activities in plants through ratiometric normalisation spatially and show its application in plants. We use measured promoter activity over a reference promoter in vivo through dual-nuclear fluorescent protein expression in Marchantia polymorpha gemmae, vegetative reproductive buds with stable cellular arrangements, which have fluorescently labelled membranes for spatially determining promoter activity. Spatial ratiometric analysis allows extruding measures for intrinsic properties of promoters and map their activities to cells and tissues. This enables comparing promoters in a range of different contexts, therefore improving our description of tissue-specific promoter activity in multicellular systems.