Biology subjects

Moinet, S.

Publications and source records attributed to Moinet, S..

2 recordsLinked to original sources

bioRxiv2026

Delta/Notch signaling level is decoded through transcriptional burst duration during muscle progenitor specification

The ability of progenitor cells to interpret different levels of signaling pathway activity is fundamental to the generation of cellular diversity during development. Muscle progenitors, for example, are exposed to different levels of signals from their microenvironment. However, how they decode these quantitative differences to regulate their cellular behaviors during myogenesis remains poorly understood. Here, we addressed this question during the specification of two populations of Drosophila adult muscle progenitors (AMPs). We found that, despite being spatially adjacent, indirect flight muscle (IFM) and direct flight muscle (DFM) progenitors receive distinct levels of Notch signaling. We further show that the spatial distribution of epithelial Delta contributes to differential Notch activation. Higher Delta levels adjacent to IFM progenitors promote stronger Notch signaling. To investigate how these quantitative differences are translated into transcriptional responses, we developed a Notch-responsive MS2 reporter to monitor transcription in living AMPs. Our measurements reveal that Notch-dependent transcription occurs in stochastic bursts, with IFM progenitors displaying longer but less frequent bursts than DFM progenitors. Strikingly, equalizing epithelial Delta levels abolished differences between the two populations in both Notch-dependent transcriptional activity and the protein levels of Notch target genes. Together, our findings suggest that quantitative differences in signaling may be translated into distinct transcriptional outputs through modulation of transcriptional bursting. This may represent a mechanism by which a single signaling pathway can be deployed to regulate diverse cellular responses during development.

developmental biology↗

bioRxiv2026

Genome-wide discovery of cis-regulatory elements in a large genome

Identifying non-coding regulatory elements in the genome poses a challenge in most organisms. Classical methods rely on trial and error to test the regulatory activities of DNA fragments using reporter constructs. In large eukaryotic genomes, where cis-regulatory elements can spread over long distances, separated by large stretches of non-functional DNA, this trial and error approach is particularly challenging. Here, we generate two types of resources that can be used to narrow the search for such cis-regulatory elements in the 3.6 Gbp genome of Parhyale hawaiensis (comparable in size to the human genome). First, we use bulk ATAC-seq to uncover genome-wide patterns of chromatin accessibility in embryonic and adult tissues of Parhyale (whole embryos and legs), and single-nucleus ATAC-seq to identify regions of open chromatin in diverse cell types recovered from adult legs, including epidermal, neuronal, muscle and blood cells. Second, by sequencing the genomes of three congeneric species of Parhyale hawaiensis - P. darvishi, P. aquilina and P. plumicornis - we identify islands of sequence conservation across the genome, corresponding to DNA elements that are functionally constrained during evolution. We present an approach by which low-coverage (10-15x) short-read genome sequencing, without genome assembly, is sufficient to provide reliable maps of sequence conservation. This approach cuts the cost and labour required to generate these maps, making the identification of cis-regulatory elements more widely accessible. We demonstrate the utility of these resources by identifying cis-regulatory elements that drive robust expression of fluorescent reporters ubiquitously and in specific cell types.

developmental biology↗