Analysis of Transcript Expression and Core Promoter DNA Sequences of Brain, Adipose Tissues and Testis in Human and Fruit Fly

Gene expression plays a fundamental role in defining the characteristics of living organisms. To deepen our understanding of tissue-specific gene expression, we analyzed transcript variant enrichment across different tissues in human and Drosophila melanogaster. Datasets are widely accessible for both of these organisms. Given the substantial volume of available information, we have focused our interest on three fundamentally distinct tissues: the brain, where both neuronal and glial cells exhibit a relatively high cellular surface area, thus requiring a large amount of lipids; the adipose tissue, which is well-known for lipid storage; and the testis, which contains a massive number of developing spermatids with high membrane requirement. These three organs have fundamental differences in their structure and function yet share some common features; they all have lipid-rich cells and have special metabolic pathways. Most studies focus on gene expression, and transcript level analyses are less common; therefore, we aimed to characterize the transcript profiles of these tissues and examine evolutionarily conserved pathways between humans and Drosophila. Additionally, we analyzed the flanking sequences of transcriptional start sites of tissue-enriched transcripts. Our findings suggest that Drosophila tissues exhibit more distinct regulation of gene expression in individual tissues (weaker correlation in expression and variable nucleotide content in core promoter), whereas human gene expression is more generalized, likely relying more heavily on distal regulatory elements for tissue-specific expression. Through network analysis, summarizing tissue specificity, physical interactions, and orthologue data, we identified shared central pathways among these tissues. A relatively large network was observable in the testis, where the ubiquitin proteasome system, various kinases and transcription factors showed central position in both organisms. Additionally, we highlighted the evolutionary potential of highly enriched testis-specific transcripts. This work provides valuable insights into the mechanisms underlying tissue-specific gene expression and evolutionary conservation.