Biology subjects

Lajoignie, D.

Publications and source records attributed to Lajoignie, D..

3 recordsLinked to original sources

bioRxiv2025

Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity

The spatiotemporal expression of developmental genes is regulated by the interplay of two key regulatory elements: core promoters, generally assumed to support only basal transcription, and enhancers, which enable their tissue- and stage-specific activation. Here, we show that spatiotemporal specificity can also be encoded within the core promoter. Using the Drosophila twist E3 enhancer as a model, we found that E3 is pleiotropic and activates four functionally unrelated genes. Despite receiving the same enhancer input, each target gene displays distinct and non-overlapping expression patterns. We demonstrate that the selective activation of each target gene is encoded within their promoter regions. Core promoters act as "gatekeepers" that restrict enhancer input into precise tissue- and stage-specific transcription, while proximal-promoter elements facilitate enhancer responsiveness. We propose that promoters function as active interpreters rather than passive recipients of enhancer signals, providing a critical but under-appreciated layer of regulatory specificity within complex gene expression programs.

genetics↗

bioRxiv2024

Spatial reconstruction of single-cell enhancer activity in a multicellular organism

Enhancers play an essential role in developmental processes by orchestrating the spatial and temporal regulation of gene expression. However, mapping the location of these regulatory elements in the genome and precisely characterizing their spatial and temporal activity remain important challenges. Here we introduce a novel in vivo and in silico method for spatial single-cell enhancer-reporter assays (spatial-scERA) designed to reconstruct the spatial activity of multiple candidate enhancer regions in parallel in a multicellular organism. Spatial-scERA integrates massively parallel reporter assays coupled with single-cell RNA sequencing (scRNA-seq) and spatial reconstruction using optimal transport, to map cell-type-specific enhancer activity at the single-cell level on a 3D virtual representation of the sample. We evaluated spatial-scERA in stage 6 Drosophila embryos using 25 candidate enhancers (including 19 uncharacterized regions), and validated the robustness of our predicted reconstructions by comparing them to microscopy images generated by in situ hybridization. Remarkably, spatial-scERA faithfully reconstructed the spatial activity of these enhancers, even when the enhancer-reporter construct was expressed in as few as 10 cells. Our results demonstrate the importance of integrating transcriptomic and spatial data for the accurate prediction of enhancer activity patterns in complex multicellular samples. Indeed, we found that chromatin modifications and open chromatin regions are often poor predictors of enhancer activity. Moreover, spatial data can often be essential for the accurate annotation of scRNA-seq clusters. Finally, we showed that spatial-scERA could be a powerful tool to link enhancers with their potential target genes. Overall, spatial-scERA provides a scalable approach to map spatio-temporal enhancer activity at single-cell resolution without the need for imaging or a priori knowledge of embryology and can be applied to any multicellular organism amenable to transgenesis.

genomics↗

bioRxiv2022

Enhancer-promoter interactions form independently of genomic distance and are functional across TAD boundaries

Developmental enhancers are essential regulatory elements that drive precise spatio-temporal gene expression patterns. They do so by interacting with the promoter of their target genes, often across large genomic distances, in a highly specific manner. However, it is unclear how such specificity can be achieved. While several studies have suggested that Topologically Associating Domains (TADs)1-3 facilitate and constrain enhancer-promoter interactions, the role of TAD boundaries in effectively restricting enhancer-promoter interactions is heavily debated. Here we show that enhancers can establish long-range interactions across TAD boundaries and even between different chromosomes. Moreover, some of these interactions are functional in vivo, illustrating their functional importance. Using the twist locus in Drosophila embryos, we systematically relocated one of its enhancers to different regulatory contexts and distances from the twist promoter. We found that the twist promoter can engage in functional enhancer-promoter interactions across a TAD boundary and that distal interactions are sometimes favored over proximal ones. Our results demonstrate that TAD boundaries are not sufficient to constrain enhancer-promoter interactions and that the formation of long-range interactions is not solely driven by distance. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.

genomics↗