Boundaries between tissues are important for establishing correct patterning during development and must be able to resist forces generated in the tissue from processes such as cell division. In a new study, Veronica Castle, Rodrigo Fernandez-Gonzalez, Gonca Erdemci-Tandogan and colleagues combine computational modelling with in vivo experiments to investigate how cell divisions impact the boundary between the ectoderm and mesectoderm tissue in the Drosophila embryo. To find out more, we spoke to first author Veronica Castle and co-corresponding authors Rodrigo Fernandez-Gonzalez, Professor at the University of Toronto, Canada, and Gonca Erdmeci-Tandogan, Assistant Professor at the University of Western Ontario, Canada.
Chromatin organization, through the assembly of DNA with histones and the folding of nucleosome chains, regulates DNA accessibility for transcription, DNA replication and repair. Although models derived from in vitro studies have proposed distinct nucleosome chain geometries, the organization of chromatin within the crowded cell nucleus remains elusive. Using cryo-electron tomography of thin vitreous sections, we directly observed the path of nucleosomal and linker DNA in situ from a flash-frozen organism - Drosophila embryos. We quantified linker length and curvature, characterizing an irregular zig-zag chromatin-folding motif, with a low degree of linker bending. Nucleosome conformations could be identified on individual particles in favorable orientations without structure averaging. Additionally, we observed particles that accommodate a number of DNA gyres ranging from less than one to up to three, which resemble previously proposed non-octameric nucleosomal particles with variable DNA wrapping.
In many animals, primordial germ cells are transiently segregated outside the somatic-cell cluster that forms the embryo’s body during early embryogenesis. This physical segregation of the germline from the soma has long been believed to be crucial for germline development, but the mechanisms controlling this segregation and its developmental significance remain unclear. Here, in Drosophila, we show that somatic gene silencing in the germline is essential for maintaining this segregation. Primordial germ cells (pole cells) lacking the Nanos- and Polar granule component (Pgc)-dependent dual repression mechanism misexpress widespread somatic genes. They form abnormal cellular protrusions, invade adjacent somatic epithelium, and intermingle with somatic cells. These mislocalized pole cells ultimately undergo cell death, whereas properly segregated cells survive. Notably, knockdown of miranda (mira), one of the somatic genes ectopically expressed, rescues these phenotypes. Our findings uncover a previously unrecognized mechanism whereby somatic gene silencing safeguards the physical boundary between the germline and the somatic cells forming the embryo’s body, highlighting its potential role in ensuring germline viability during early development.
Promoter architecture plays a central role in transcriptional regulation, yet predicting promoter activity directly from DNA sequence remains challenging. Here, we assess whether transformer-based DNA language models can learn and interpret regulatory logic encoded in Drosophila core promoters. We fine-tuned the 117-million-parameter DNABERT-2 model on ~700 synthetic promoters assayed by ~2,600 dual-luciferase measurements in Drosophila S2 cells. A sequence-only model achieved high predictive accuracy (R2 ≈ 0.91), demonstrating that core promoter sequence alone strongly constrains transcriptional output. Model interpretability using SHapley Additive exPlanations (SHAP) revealed biologically meaningful sequence features corresponding to canonical core promoter elements. Extending the model to incorporate biological context, including Ecdysone (Ecd) hormonal activation and flanking -1/+1 nucleosomal sequences, preserved strong performance while capturing more complex promoter behavior. Gene-wise cross-validation showed robust generalization for most promoters, and application to independent in vivo embryo data demon-strated that the model still generalizes reasonably well, even in complex biological contexts. ### Competing Interest Statement The authors have declared no competing interest.
Somatic homolog pairing is a defining feature of the diploid genome organization in Drosophila and underlies its transvection-based gene regulation. Here, to understand the physical effect of homolog pairing on the resulting three-dimensional (3D) organization, we employ the heterogeneous loop model and reconstruct 3D structures of the Drosophila embryo genome based on its haplotype-resolved Hi-C data. The resulting structures reveal robust end-to-end juxtaposition between homologous chromosomes amid substantial cell-to-cell variability. On sub-megabase scales, tight pairing between homologous loci at domain boundaries give rise to significant coincidence between cis and trans -homolog domain boundaries in the Hi-C map, while interior regions remain loosely associated. To uncover the physical origin of this organization, we compare the contact maps resulting from the polymer models implementing specific and non-specific button-mediated pairing mechanisms with Hi-C, finding that the intra-chromosomal contacts constrained by specifically paired inter-chromosomal buttons give rise to pairing-induced domains (PIDs). Our study suggests specific adhesive interactions as a central organizing principle of the diploid genome in Drosophila embryos. ### Competing Interest Statement The authors have declared no competing interest. Zhejiang Provincial Natural Science Foundation, LQ22B040001 Zhejiang Sci-Tech University, https://ror.org/03893we55, 20062226-Y Korea Institute for Advanced Study, https://ror.org/041hz9568, CG035003
flypapers