Genomic context sensitizes regulatory elements to genetic disruption

• Published in: Molecular cell Vol. 84; no. 10; pp. 1842 - 1854.e7
• Main Authors: Ordoñez, Raquel, Zhang, Weimin, Ellis, Gwen, Zhu, Yinan, Ashe, Hannah J., Ribeiro-dos-Santos, André M., Brosh, Ran, Huang, Emily, Hogan, Megan S., Boeke, Jef D., Maurano, Matthew T.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 16.05.2024
• Subjects: Animals; CCCTC-Binding Factor - genetics; CCCTC-Binding Factor - metabolism; DNA; Enhancer Elements, Genetic; enhancer selectivity; gene regulation; genetic engineering; genome; genome writing; Genomic Imprinting; genomic regulatory architecture; genomics; Genomics - methods; insulin-like growth factor II; Insulin-Like Growth Factor II - genetics; Insulin-Like Growth Factor II - metabolism; loci; Locus Control Region - genetics; Mice; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; SOXB1 Transcription Factors - genetics; SOXB1 Transcription Factors - metabolism; synthetic regulatory genomics; genome writing; enhancer selectivity; gene regulation; genomic regulatory architecture; genetic engineering; synthetic regulatory genomics
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2024.04.013

Genomic context critically modulates regulatory function but is difficult to manipulate systematically. The murine insulin-like growth factor 2 (Igf2)/H19 locus is a paradigmatic model of enhancer selectivity, whereby CTCF occupancy at an imprinting control region directs downstream enhancers to activate either H19 or Igf2. We used synthetic regulatory genomics to repeatedly replace the native locus with 157-kb payloads, and we systematically dissected its architecture. Enhancer deletion and ectopic delivery revealed previously uncharacterized long-range regulatory dependencies at the native locus. Exchanging the H19 enhancer cluster with the Sox2 locus control region (LCR) showed that the H19 enhancers relied on their native surroundings while the Sox2 LCR functioned autonomously. Analysis of regulatory DNA actuation across cell types revealed that these enhancer clusters typify broader classes of context sensitivity genome wide. These results show that unexpected dependencies influence even well-studied loci, and our approach permits large-scale manipulation of complete loci to investigate the relationship between regulatory architecture and function. [Display omitted] •Composite enhancer elements are subject to specific genomic context effects•The H19 enhancer cluster relies on regulatory elements outside the canonical Igf2/H19 locus•The Sox2 LCR functions autonomously of its surrounding context•Deletion or repositioning regulatory elements increases locus sensitivity to genomic context Genomic context plays a key role in regulatory function but is difficult to manipulate systematically. Ordoñez et al. use synthetic regulatory genomics to manipulate regulatory architecture on a large scale, revealing unexpected context dependencies that influence even the most studied functional elements.