Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes.

ABSTRACT: Descriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specif

SUBMITTER: Company C 

PROVIDER: S-EPMC10844330 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature