RegDesign-Bench: Benchmarking computational methods for cell-type-specific regulatory DNA design

Abstract

The de novo design of regulatory DNA sequences that drive cell-type-specific gene expression could enable precise gene control in synthetic biology, cell engineering and gene therapy. Various computational methods have been developed for this task, yet systematic comparisons that guide method selection for different design objectives remain limited. Here, we introduce RegDesign-Bench, a standardized framework for evaluating cell-type-specific cis-regulatory element design through a comprehensive set of computational analyses. Among the methods tested, strong predicted activity was not consistently accompanied by cell-type-selective accessibility or prominent cell-type-associated motif signals. Similarity to reference sequence distributions also did not ensure high predicted target-cell activity or specificity. These findings demonstrate that favourable performance on individual measurements does not necessarily extend across regulatory properties and library characteristics, revealing application-dependent strengths and limitations of current design methods. Overall, RegDesign-Bench offers a general-purpose computational framework for comparing and selecting methods to design regulatory DNA that drives cell-type-specific gene expression.