Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide.

ABSTRACT:

Background

Massively parallel reporter assays (MPRAs) and self-transcribing active regulatory region sequencing (STARR-seq) have revolutionized enhancer characterization by enabling high-throughput functional assessment of regulatory sequences.

Results

Here, we systematically evaluate six MPRA and STARR-seq datasets generated in the human K562 cell line and find substantial inconsistencies in enhancer calls from different labs that are primarily due to technical variations in data processing and experimental workflows. To address these variations, we implement a uniform enhancer call pipeline, which significantly improve cross-assay agreement. While increasing sequence overlap thresholds enhanced concordance in STARR-seq assays, cross-assay consistency in LentiMPRA is strong

SUBMITTER: Zhang J 

PROVIDER: S-EPMC12581240 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature