<> "The repository administrator has not yet configured an RDF license."^^ . <> . . "Developmental constraints and the\r\nregulatory logic of Drosophila enhancers"^^ . "Summary\r\nEnhancers can generate specific patterns of gene expression, which are essential\r\nfor organismal development. Despite decades of research, how enhancers encode\r\nthe information necessary to drive these precise patterns remains unclear. To\r\naddress this question, in this project, I focused on the interplay of two different\r\napproaches: 1) Using well-known endogenous enhancers, I searched for putative\r\nmissing regulatory elements by integrating information from different mutational\r\nscreenings, and 2) Using the combination of synthetic enhancers expression profiles\r\nand thermodynamic models, I tested the possibility of several mechanisms of their\r\nassociated Transcription Factors (TFs). In the first approach, I focused on two of\r\nthe best-characterized animal enhancers, the minimal stripe 2 enhancer (MS2E)\r\nand the E3N enhancer. The MS2E enhancer can generate the second of the seven\r\nstripes of the Even-skipped gene expression pattern. The E3N enhancer regulates\r\nthe expression of the Shavenbaby gene, which has an eight-striped pattern. For the\r\nMS2E enhancer, a systematic and targeted mutagenesis screening was performed\r\nand analyzed, while for the E3N enhancer, I analyzed data from a randomized\r\nmutagenesis approach. For both enhancers, I estimated and associated affinity\r\nchanges of multiple TF binding sites (TFBSs) with the observed expression phe-\r\nnotypes. A dense encoded architecture was observed for the two enhancers where\r\nalmost each mutated section generates a phenotype that differs from the wild-type.\r\nAffinity changes and motif turnover analyses of known TFBSs could explain only\r\na small fraction of these phenotypes. Finally, I explored experimental alterna-\r\ntives for finding additional associated TFs and the evolutionary implications of a\r\ndense encoded enhancer architecture. These results suggest the need to find ad-\r\nditional regulators and improve current versions of the binding profiles of already\r\nknown TFs. In the second approach, I evaluated the roles of early patterning\r\nTFs through synthetic enhancers and mechanistic modeling. I observed that early\r\nembryonic enhancers are associated with higher information at the sequence level\r\ncomposition than later and synthetic random enhancers. Additionally, the syn-\r\nthetic system could encode different sharp gene expression patterns with different\r\ncombinations of known TFBSs. The results from implementing generalized ther-\r\nmodynamic models suggested that these TFs are highly context-dependent. This\r\nanalysis suggested multiple equally performing mechanisms for different possibili-\r\nties for TF-TF interactions, TF function, and modes of regulation. These models\r\ncould predict observed expression patterns, such as a broad stripe in the center\r\nof the embryo, but other expression patterns, such as the presence of additional\r\nanterior expression, could not be explained. Finally, I propose alternative mecha-\r\nnisms by which known TFs work in this context and new directions for enhancer\r\ndesign to expand the understanding of encoding developmental patterns."^^ . "2025" . . . . . . . "Gilberto Alejandro"^^ . "Alvarez Canales"^^ . "Gilberto Alejandro Alvarez Canales"^^ . . . . . . "Developmental constraints and the\r\nregulatory logic of Drosophila enhancers (PDF)"^^ . . . "22_July_PhDThesis_GilbertoAlvarez_printed_version.pdf"^^ . . . "Developmental constraints and the\r\nregulatory logic of Drosophila enhancers (Other)"^^ . . . . . . "indexcodes.txt"^^ . . . "Developmental constraints and the\r\nregulatory logic of Drosophila enhancers (Other)"^^ . . . . . . "lightbox.jpg"^^ . . . "Developmental constraints and the\r\nregulatory logic of Drosophila enhancers (Other)"^^ . . . . . . "preview.jpg"^^ . . . "Developmental constraints and the\r\nregulatory logic of Drosophila enhancers (Other)"^^ . . . . . . "medium.jpg"^^ . . . "Developmental constraints and the\r\nregulatory logic of Drosophila enhancers (Other)"^^ . . . . . . "small.jpg"^^ . . "HTML Summary of #36747 \n\nDevelopmental constraints and the \nregulatory logic of Drosophila enhancers\n\n" . "text/html" . . . "570 Biowissenschaften, Biologie"@de . "570 Life sciences"@en . .