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Mapping regulatory elements from transcription initation data

ABSTRACT: Mapping regulatory elements from transcription initation data

PROVIDER: PRJNA1314037 | ENA |

REPOSITORIES: ENA

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Mapping regulatory elements from transcription initation data

Project description: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.

2025-09-02 | GSE306952 | GEO

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