<> "The repository administrator has not yet configured an RDF license."^^ . <> . . "Single-cell dissection of regulatory landscapes during embryogenesis"^^ . "Gene regulatory networks control the precise spatial and temporal execution of\r\ndevelopmental gene expression programs during embryogenesis. Enhancers are core\r\ncomponents of these regulatory networks and they serve as integration platforms for\r\nthe developmental signals delivered by transcriptions factors (TFs). Dissecting the\r\nfunction of gene regulatory networks and their underlying components is a major goal\r\nof modern biology. In this thesis, I leverage the recent advances in single-cell genomics\r\nmethods to assess the impact of perturbations on developmental regulatory networks,\r\nusing Drosophila melanogaster embryogenesis as a well-studied model system.\r\n\r\nI started by optimizing a protocol to profile single-cell chromatin accessibility by sci-\r\nATAC-seq in Drosophila embryos and applied it to profile a dense time-course of over\r\n20,000 cells during mesoderm development. The time-course comprised eight\r\noverlapping time-points spanning half of embryogenesis and captured a continuum of\r\nregulatory transitions as cells move from multipotency to different developmental\r\nlineages. I used this dataset to reconstruct developmental trajectories of all major celltypes,\r\nand uncover both the TFs and enhancers involved.\r\n\r\nI then present two approaches that integrate the single-cell resolution of sci-ATAC-seq\r\nwith perturbations of TFs and enhancers, as a means to dissect regulatory networks.\r\nFirst, I perturbed regulatory networks in trans, by mutating four key developmental TFs\r\nthat drive Drosophila mesoderm development and used sci-ATAC-seq to jointly assess\r\nthe regulatory outcome at both the cellular and molecular level. I demonstrate that this\r\napproach not only recovers previously described high-level phenotypes, but also more\r\nsubtle alterations in cell fate, while simultaneously providing information on the TF’s\r\ninput at enhancers. Second, I perturbed regulatory networks in cis by exploiting natural\r\nsequence variation as a means for large-scale enhancer disruption. By profiling\r\nchromatin accessibility in hybrid embryos obtained from mating genetically diverse\r\nparent lines, I show how sci-ATAC-seq can be used to discover the cellular context\r\naffected by genetic variants and I discuss upcoming in vivo experiments to assess their\r\nimpact on enhancer activity."^^ . "2022" . . . . . . . "Stefano"^^ . "Secchia"^^ . "Stefano Secchia"^^ . . . . . . "Single-cell dissection of regulatory landscapes during embryogenesis (PDF)"^^ . . . "Stefano_Secchia_Thesis_Final.pdf"^^ . . . "Single-cell dissection of regulatory landscapes during embryogenesis (Other)"^^ . . . . . . "indexcodes.txt"^^ . . . "Single-cell dissection of regulatory landscapes during embryogenesis (Other)"^^ . . . . . . "lightbox.jpg"^^ . . . "Single-cell dissection of regulatory landscapes during embryogenesis (Other)"^^ . . . . . . "preview.jpg"^^ . . . "Single-cell dissection of regulatory landscapes during embryogenesis (Other)"^^ . . . . . . "medium.jpg"^^ . . . "Single-cell dissection of regulatory landscapes during embryogenesis (Other)"^^ . . . . . . "small.jpg"^^ . . "HTML Summary of #30776 \n\nSingle-cell dissection of regulatory landscapes during embryogenesis\n\n" . "text/html" . .