Gene expression regulation involves intricate genetic and environmental interactions that shape phenotypic diversity. This dissertation explores both intraspecific and interspecific regulatory variation using F1 hybrid models in Drosophila. The first part of the study focuses on Drosophila melanogaster, characterizing cis- and trans-regulatory effects within the species. By combining allele-specific mapping and RNA sequencing, the analysis reveals that cis-regulatory effects are predominant, driving much of the variation in gene expression. Trans-regulatory effects, while less frequent, may indicate complex interactions between regulatory elements.The second part extends the investigation to interspecific gene regulation between Drosophila melanogaster and Drosophila simulans. By integrating ribosome profiling with RNA sequencing, the study evaluates both transcriptional and translational divergence in hybrid offspring. This analysis identifies significant differences in both cis- and trans-regulatory effects, with trans effects contributing prominently to translation efficiency variation. Temperature-dependent changes further modulate both transcription and translation, highlighting the role of environmental factors in regulatory divergence between species. Overall, the findings demonstrate that gene expression regulation is shaped by both local genetic elements and broader regulatory networks, modulated by environmental conditions. The comparative analysis of intraspecific and interspecific hybrids provides insights into the evolutionary dynamics of gene regulation, emphasizing the buffering role of translational regulation and the adaptive potential of trans-regulatory elements. This comprehensive framework enhances our understanding of gene expression regulation and its implications for evolutionary biology.
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