Natural environmental factors and anthropogenic disturbances can modulate gene expression,resulting in alteration of organismal phenotype. In the first part of my thesis project, I used Drosophila melanogaster as a model to understand the mechanisms by which 24-hour light-dark cycles can regulate rhythmic changes in the chromatin to generate circadian rhythms of gene expression and orchestrate daily biological rhythms in insects. I observed that two circadian clock proteins, CLOCK and TIMELESS, regulate daily rhythmicity in the binding of BRAHMA, a chromatin remodeler, to DNA spanning clockcontrolled genes to facilitate their rhythmic gene expression cycles. Moreover, because TIMELESS degrades in the presence of light, my results provide new insights into how light affects DNA structure and gene expression. In the second part of my thesis project, I investigated the molecular mechanisms by which the fruit pest Drosophila suzukii adapt to insecticide applications and develop resistance. Specifically, I performed RNA sequencing analysis on D. suzukii flies that are either susceptible or resistant to common insecticides to determine genetic mechanisms underlying insecticide resistance in this agricultural pest. My results revealed that enhanced metabolic detoxification confers pyrethroid resistance while spinosad resistance is the result of both metabolic and penetration resistance. Finally, we identified alternative splicing as a potential mechanism of resistance. My results will facilitate the development of efficient molecular diagnostics to monitor insecticide resistance development in the field and enable growers to develop more informed D. suzukii spray programs to control this devastating pest more effectively.