Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

Although enhancers are central regulators of mammalian gene expression, the mechanisms underlying enhancer-promoter (E-P) interactions remain unclear. Chromosome conformation capture (3C) methods effectively capture large-scale three-dimensional (3D) genome structure but struggle to achieve the depth necessary to resolve fine-scale E-P interactions. Here, we develop Region Capture Micro-C (RCMC) by combining micrococcal nuclease (MNase)-based 3C with a tiling region-capture approach and generate the deepest 3D genome maps reported with only modest sequencing. By applying RCMC in mouse embryonic stem cells and reaching the genome-wide equivalent of similar to 317 billion unique contacts, RCMC reveals previously unresolvable patterns of highly nested and focal 3D interactions, which we term microcompartments. Microcompartments frequently connect enhancers and promoters, and although loss of loop extrusion and inhibition of transcription disrupts some microcompartments, most are largely unaffected. We therefore propose that many E-P interactions form through a compartmentalization mechanism, which may partially explain why acute cohesin depletion only modestly affects global gene expression. Region Capture Micro-C (RCMC) combines MNase-based 3C with a tiling region-capture method. Profiling mouse embryonic stem cells with RCMC identifies nested microcompartments, which connect enhancers and promoters.

Automated summary

The researchers developed a method called Region Capture Micro-C (RCMC), which combines MNase-based 3C with a tiling region-capture approach to generate deep 3D genome maps. Using RCMC in mouse embryonic stem cells, they discovered previously unresolvable patterns of highly nested and focal 3D interactions, termed microcompartments, which frequently connect enhancers and promoters. Most microcompartments are largely unaffected by loss of loop extrusion and transcription inhibition, suggesting that many enhancer-promoter interactions form through a compartmentalization mechanism.