The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
Nat Commun. 2024 Sep 27;15(1):8350. doi: 10.1038/s41467-024-52599-6.
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.
调控基因组学的一个关键问题是顺式调控元件（CREs）是可以在基因组中的任何位置发挥作用的模块化元件，还是它们适应于某些特定的基因组位置。为了区分这两种可能性，我们开发了 MPIRE（大规模并行集成调控元件），这是一种在基因组中数千个定义位置上平行重复检测 CRE 的技术。MPIRE 使我们能够将 CRE 的固有活性与其基因组环境的影响区分开来。我们应用 MPIRE 在数千个基因组位置上检测了三个绝缘子序列，发现每个绝缘子在具有可区分特征的位置发挥作用。这三个绝缘子都可以阻断增强子，但每个绝缘子都在特定位置阻断特定的增强子。然而，只有 ALOXE3 似乎可以阻断异染色质沉默。我们的结论是，绝缘子的功能高度依赖于上下文，MPIRE 是一种揭示 CRE 上下文依赖性的强大方法。
