The e2MPRA technology simultaneously assesses the regulatory activities and epigenetic modifications of multiple cis-regulatory elements, allowing the systematic characterization of gene regulation.
Effect estimate: HR 0.76 (95% CI 0.68-0.85)
p-value: p=<0.001
Abstract Using various biochemical assays that identify transcription factor (TF) binding and histone modifications, cis -regulatory elements (CREs) can be annotated in a genome-wide manner. However, these assays are descriptive and require functional validation. To the best of our knowledge, no technology can simultaneously analyze the regulatory function and epigenomic modifications of a specific sequence. Here, we develop an enrichment followed by epigenomic profiling massively parallel reporter assay (e2MPRA). This technique uses lentivirus to enrich for the integration of specific CREs into the genome and applies MPRA, Cut&Tag or ATAC-seq on them enabling simultaneous, high-throughput analysis of regulatory activity, protein binding, and epigenetic modification. We demonstrate that e2MPRA can dissect the epigenetic functions of TF motifs arranged within synthetic enhancers and evaluate the effects of sequence perturbation on epigenetic states. In summary, e2MPRA advances our understanding of the regulatory code, its effect on the epigenome and how its alteration leads to phenotypic effects.
Zhang et al. (Wed,) conducted a other in cis-regulatory elements (CREs) and their genetic variation effects. e2MPRA vs. Negative controls include random genomic sequences and scrambled sequences. was evaluated on Regulatory activity measured by transcriptional activity from MPRA and epigenetic modifications assessed through ATAC-seq and CUT&Tag. (HR 0.76, 95% CI 0.68-0.85, p=<0.001). The e2MPRA technology simultaneously assesses the regulatory activities and epigenetic modifications of multiple cis-regulatory elements, allowing the systematic characterization of gene regulation.