Trans-acting Determinants of Gene Expression: Effects of Transcription Factor Affinity, Abundance, and Localization

Abstract Transcription factors (TFs) regulate gene expression by binding cis-regulatory DNA elements, yet how trans-regulatory characteristics such as TF affinity, concentration, and localization interact with cis-regulatory elements remains largely unclear. We systematically analyzed TF affinity mutants across abundance, and localization states and found that promoter binding-site strength most readily modulated expression levels, followed by TF localization and concentration, while affinity variations were mainly buffered. We further uncover performance trade-offs between TF abundance, localization, and affinity. Together, these results reveal how trans and cis factors collectively shape gene-regulatory output.