PINTS

PINTS identifies active promoters and enhancers genome-wide by mapping exact 5' transcription start sites (TSSs) of nascent transcripts to detect enhancer RNAs (eRNAs) using genome-wide RNA-seq data including GRO/PRO-cap.

Key Features:

• Enhancer RNA detection: Uses nuclear run-on followed by cap-selection assays (GRO/PRO-cap) to detect enhancer RNAs (eRNAs).
• Precise TSS mapping: Pinpoints exact 5' transcription start sites (TSSs) of nascent transcripts to resolve promoter and enhancer activity.
• Enhancer TSS compendium: Compiles candidate enhancer TSSs detected across over 120 cell and tissue types.
• Assay benchmarking: Compares 13 different RNA-seq assays in K562 cells and identifies GRO/PRO-cap as optimal for eRNA and active enhancer detection.
• Genome-wide RNA-seq integration: Integrates genome-wide RNA-seq assays to identify transcription start sites at scale.

Scientific Applications:

• Active enhancer identification: Identification of active promoters and enhancers via mapped nascent TSSs and eRNA signals.
• Functional characterization: Provides TSS-resolved data to support studies of enhancer-promoter relationships and regulatory element function.
• Cross-tissue analysis: Enables comparative analysis of enhancer activity across multiple cell types and tissues using the compiled TSS dataset.

Methodology:

Integrates genome-wide RNA-seq assays; compares 13 RNA-seq assays in K562 cells and optimizes use of GRO/PRO-cap (nuclear run-on plus cap selection) for eRNA detection and active enhancer identification.