Massively parallel characterization of insulator activity across the genome

• Published in: Nature communications Vol. 15; no. 1; pp. 8350 - 14
• Main Authors: Hong, Clarice K. Y., Wu, Yawei, Erickson, Alyssa A., Li, Jie, Federico, Arnold J., Cohen, Barak A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27.09.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/47; 49; 631/208/191; 631/208/200; 631/553/552; Animals; Assaying; Context; Enhancer Elements, Genetic - genetics; Enhancers; Gene sequencing; Genome - genetics; Genomes; Genomics; Genomics - methods; Heterochromatin; Heterochromatin - genetics; Heterochromatin - metabolism; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Insulator Elements - genetics; Insulators; Mice; multidisciplinary; Regulatory sequences; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• 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. Here, the authors investigate how cis-regulatory elements (CRE) function in diverse genomic locations. They develop a high-throughput method to assay CRE activity across the genome and apply it to reveal the context dependencies of insulator activity.