Genomic context sensitizes regulatory elements to genetic disruption

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Genomic context is crucial for gene regulatory function.
• The mouse Igf2/H19 locus serves as a model for enhancer selectivity, controlled by CTCF.
• Understanding locus architecture is key to deciphering gene regulation.

Purpose of the Study:

• To systematically dissect the architecture of the Igf2/H19 locus using synthetic regulatory genomics.
• To identify previously uncharacterized long-range regulatory dependencies.
• To investigate enhancer selectivity and context sensitivity genome-wide.

Main Methods:

• Utilized synthetic regulatory genomics to replace the native Igf2/H19 locus with large payloads.
• Performed enhancer deletion and ectopic delivery experiments.
• Analyzed regulatory DNA actuation across diverse cell types.

Main Results:

• Revealed previously unknown long-range regulatory dependencies at the native Igf2/H19 locus.
• Demonstrated that H19 enhancers require native surroundings, while the Sox2 locus control region (LCR) functions autonomously.
• Identified enhancer clusters as representative of broader context sensitivity in the genome.

Conclusions:

• Unexpected regulatory dependencies impact even well-studied genetic loci.
• Synthetic genomics enables large-scale manipulation of complete loci for functional studies.
• The study provides a framework for investigating the relationship between regulatory architecture and function.