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Mapping regulatory elements from transcription initation data

ABSTRACT: Determining enhancer and promoter activities is important for modeling gene regulation and interpreting the impact of genetic variation on disease. Studying regulatory element activity genome-wide has been challenging, partly due to a lack of benchmarks. Here, we systematically evaluate CAGE for detecting active regulatory elements and present PRIME, a framework for analyzing regulatory elements from transcription initiation data. We assess nuclear RNA CAGE (nucCAGE) versus total RNA CAGE using fine-mapped eQTLs, likely pathogenic variants, and CRISPRi loci. Transcribed loci identified by PRIME on CAGE data show superior performance in detecting active regulatory elements compared to transcription run-on assays, and nucCAGE improves recall. Importantly, nucCAGE maintains the ability of CAGE to study promoter activities at base-pair resolution. These assays and computational tools will aid in understanding gene regulatory circuits and interpreting pathogenic variants.

ORGANISM(S): Homo sapiens

PROVIDER: GSE306952 | GEO | 2025/09/02

REPOSITORIES: GEO

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