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Massively parallel characterization of insulator activity across the genome

Author

Listed:
  • Clarice K. Y. Hong

    (Washington University in St. Louis
    Washington University in St. Louis)

  • Yawei Wu

    (Washington University in St. Louis
    Washington University in St. Louis)

  • Alyssa A. Erickson

    (Washington University in St. Louis
    Washington University in St. Louis)

  • Jie Li

    (Washington University in St. Louis
    Washington University in St. Louis)

  • Arnold J. Federico

    (Washington University in St. Louis
    Washington University in St. Louis)

  • Barak A. Cohen

    (Washington University in St. Louis
    Washington University in St. Louis)

Abstract

A key question in regulatory genomics is whether cis-regulatory elements (CREs) are modular elements that can function anywhere in the genome, or whether they are adapted to certain genomic locations. To distinguish between these possibilities we develop MPIRE (Massively Parallel Integrated Regulatory Elements), a technology for recurrently assaying CREs at thousands of defined locations across the genome in parallel. MPIRE allows us to separate the intrinsic activity of CREs from the effects of their genomic environments. We apply MPIRE to assay three insulator sequences at thousands of genomic locations and find that each insulator functions in locations with distinguishable properties. All three insulators can block enhancers, but each insulator blocks specific enhancers at specific locations. However, only ALOXE3 appears to block heterochromatin silencing. We conclude that insulator function is highly context dependent and that MPIRE is a robust method for revealing the context dependencies of CREs.

Suggested Citation

  • Clarice K. Y. Hong & Yawei Wu & Alyssa A. Erickson & Jie Li & Arnold J. Federico & Barak A. Cohen, 2024. "Massively parallel characterization of insulator activity across the genome," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52599-6
    DOI: 10.1038/s41467-024-52599-6
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