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Related Concept Videos

Epigenetic Regulation01:46

Epigenetic Regulation

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Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Massively Parallel Reporter Assays in Cultured Mammalian Cells
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Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.

Zicong Zhang1, Ilias Georgakopoulos-Soares2, Guillaume Bourque1,3,4,5

  • 1Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.

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|January 14, 2026
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Summary
This summary is machine-generated.

We developed e2MPRA, a new method to simultaneously analyze the regulatory function and epigenomic modifications of cis-regulatory elements (CREs). This technique advances understanding of the genome

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Genome-wide annotation of cis-regulatory elements (CREs) relies on descriptive assays for transcription factor (TF) binding and histone modifications.
  • Functional validation of CREs is essential but challenging, with no current technology enabling simultaneous analysis of regulatory function and epigenomic state.

Purpose of the Study:

  • To develop a novel technology for simultaneous, high-throughput analysis of CRE regulatory function and associated epigenomic modifications.
  • To enable functional dissection of TF motifs within synthetic enhancers and assess sequence perturbation effects on epigenetic states.

Main Methods:

  • Development of an enrichment followed by epigenomic profiling massively parallel reporter assay (e2MPRA).
  • Utilizes lentivirus for CRE enrichment and integration, coupled with MPRA, Cut&Tag, or ATAC-seq.
  • Enables simultaneous assessment of regulatory activity, protein binding, and epigenetic modifications.

Main Results:

  • Demonstrated e2MPRA's capability to dissect epigenetic functions of TF motifs in synthetic enhancers.
  • Successfully evaluated the impact of sequence perturbations on epigenetic states using e2MPRA.
  • Achieved simultaneous, high-throughput analysis of regulatory function and epigenomic modifications for specific sequences.

Conclusions:

  • e2MPRA is a powerful new technique for comprehensive analysis of cis-regulatory elements.
  • The method advances understanding of the regulatory code, its impact on the epigenome, and phenotypic consequences of alterations.