Regulatory genomics during Drosophila embryogenesis: dissecting enhancer-promoter interactions

Project Information

Enhancer3D

Grant agreement ID: 759708

DOI

10.3030/759708

Project closed

EC signature date 23 November 2017

Start date 1 May 2018

End date 31 December 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 770 375,00

EU contribution

€ 1 770 375,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Periodic Reporting for period 5 - Enhancer3D (Regulatory genomics during Drosophila embryogenesis: dissecting enhancer-promoter interactions)

Reporting period: 2024-05-01 to 2024-12-31

Summary of the context and overall objectives of the project

In eukaryotes, the complex regulation of temporal- and tissue-specific gene expression is controlled by the binding of transcription factors to enhancers, which in turn interact with the promoter of their target gene(s) via the formation of a chromatin loop. Despite their importance, the properties governing enhancer function and enhancer-promoter loops in the context of the three-dimensional organisation of the genome are still poorly understood.
My recent work suggests that (i) developmental genes are often regulated by multiple enhancers, sometimes located at great linear distances, (ii) the spatio-temporal activity of a large fraction of those enhancers remains unknown, (iii) enhancer-promoter interactions are usually established before the target gene is expressed and are largely stable during embryogenesis, and (iv) stable interactions seem to be associated with the presence of paused RNA Polymerase II at the promoter before gene activation.
Building upon these results, we propose to advance to the next level in the dissection of enhancer-promoter interaction functionality in the context of Drosophila embryogenesis. Specifically, we will address three important questions:
(WP1) What determines the specificity of promoter-enhancer interactions in a complex genome?
(WP2) Are enhancer-promoter interactions tissue-specific, and what are the drivers of this specificity?
(WP3) Are all enhancer-promoter interactions functional, and how does the activity of an enhancer relate to the expression of the gene it interacts with?
To this end, my group combines state-of-the-art methods in genetics and genomics, including novel single-cell techniques, using Drosophila embryogenesis as a model system. Our results will provide a unique view of the functionality of enhancer-promoter interactions in a developing embryo, a significant step towards understanding the link between chromatin organisation and transcription regulation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

WP1: Specificity of promoter-enhancer interactions in a complex genome
We have generated a number of mutant fly lines to study the role of our enhancer of interest (called E3) which regulates the twist gene in the Drosophila embryo.
Sub-aim 1a:
In a first project, we started by deleting this enhancer. Surprisingly, the deletion is lethal, which was not expected based on previous knowledge about this enhancer.
Using enhancer-reporter assays, we were able to show that the spatio-temporal activity of this enhancer is different from the activity of the gene it regulates, opening interesting new avenues of research.
Following up on this initial result, we discovered that the E3 enhancer is pleiotropic. It does not only regulate the expression of twist, but is shared between at least 3 different genes.
Interestingly, for one of these genes, E3 drives expression in a tissue of ectodermal origin, which contrasts with twist being a mesodermal transcription factor.
Overall, we have shown that E3 is a pleiotropic enhancer that functions across germ layers and regulates the expression of multiple genes even across large genomic distances. Tissue specificity is driven by the specific sequence of each gene's promoter.
These results are currently been written up in a manuscript in preparation.
In another part of this sub-aim, we reintroduced our enhancer of interest at various locations in the genome in a context where the endogenous E3 enhancer was deleted.
Surprisingly, one of the insertion sites could rescue the lethality of the deletion although the ectopic enhancer was introduced 51kb away across a TAD boundary.
We then analyzed the effect of these mutants on chromatin organization (by 4C-seq and 3D DNA FISH) and found that the ectopic enhancer can interact with the promoter of its target gene in two of the above-mentioned lines, despite a very large distance separating them.
Bioinformatics analysis confirmed that a lot of enhancer-promoter interactions occur across TAD boundaries in the Drosophila genome. We have proven their functionality in at least one case.
These results were published in Nucleic Acids Research (Balasubramanian et al.).
We are currently following up on this work by extending the number of functional enhancer-promoter interactions to decipher the drivers of long-range inter-TAD enhancer-promoter interactions.
Sub-aim 1-b:
In a second project, we generated a number of mutants targetting important motifs in our enhancer on interests. We analyzed the effect of these mutants compared to the wild-type using qRT-PCR and immunostaining.
We also developed a high-throughput method to analyze their effect on gene expression by adapting the HCR-flowFISH method to Drosophila embryos.
We are currently analyzing the data.

WP3: Large-scale enhancer activity screen
We have developed a novel in vivo / in silico method for spatial single-cell enhancer-reporter assays (spatial-scERA) designed to reconstruct the spatial activity of candidate enhancer regions in parallel in multicellular organisms.
Spatial-scERA integrates parallel reporter assays with single-cell RNA sequencing and spatial reconstruction using optimal transport, to map cell-type-specific enhancer activity at the single-cell level on a 3D virtual sample. We evaluated spatial-scERA in Drosophila embryos using 25 candidate enhancers, and validated the robustness of our reconstructions by comparing them to in situ hybridization. Remarkably, spatial-scERA faithfully reconstructed the spatial activity of these enhancers, even when the reporter construct was expressed in as few as 10 cells. Our results demonstrate the importance of integrating transcriptomic and spatial data for accurately predicting enhancer activity patterns in complex multicellular samples and linking enhancers to 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.
These results have been published as a preprint (Alberti et al) and have been accepted upon minor revision at Nucleic Acids Research.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project allowed us to provide the first clear evidence for the presence of functional inter-TAD interactions, with a detailed characterization of their functionality in Drosophila embryos.
We have also uncovered for the first time that pleiotropic enhancers can be shared between different genes expressed in different germ layers.
Finally, we developed an innovative method that combines parallel reporter assays with single-cell RNA sequencing and spatial reconstruction using optimal transport, to map cell-type-specific enhancer activity at the single-cell level on a 3D virtual sample.

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