# Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA

## TL;DR

e2MPRA is a new method that measures both gene regulation and epigenetic changes in the same DNA sequences, helping understand how genetic variations affect traits and disease.

## Contribution

e2MPRA is the first technology to simultaneously analyze regulatory function and epigenomic modifications of specific DNA sequences.

## Key findings

- e2MPRA enables simultaneous analysis of regulatory activity and epigenetic modifications of cis-regulatory elements.
- The method can dissect the epigenetic functions of transcription factor motifs in synthetic enhancers.
- e2MPRA evaluates the effects of sequence perturbations on epigenetic states and regulatory function.

## 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.

Changes in gene regulation are a major driver of human traits and disease. Here, authors develop e2MPRA, a high-throughput technology that simultaneously measures enhancer activity and associated epigenetic modifications, revealing how sequence variants influence regulatory function.