Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes," where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.

Genomes of higher organisms are extensively folded into three-dimensional (3D) chromosome territories within the nucleus 1. Advanced 3D genome mapping methods that combine proximity ligation and high-throughput sequencing (Hi-C) 2 , plus chromatin immunoprecipitation (ChIA-PET) 3 , have revealed topologically associating domains (TADs) 4 with frequent chromatin contacts and have identified chromatin loops mediated by specific protein factors for insulation and transcriptional regulation 5-7. However, these methods rely on pairwise proximity ligation and reflect population-level views, and thus cannot reveal the detailed nature of chromatin interactions. Although single-cell Hi-C 8 could potentially overcome this issue, it may be limited by data sparsity inherent to current single-cell assays. Recent advances in microfluidics have opened new opportunities for droplet-based genomic analysis 9 , yet this approach has not been adapted to chromatin interaction analysis. Here, we describe a strategy for multiplex chromatin interaction analysis via droplet-based and barcode-linked sequencing (ChIA-Drop). We demonstrate the robustness of ChIA-Drop in capturing complex chromatin interactions with unprecedented single-Reprints and permissions information is available at www.nature.com/reprints.

No abstract

Farnesylation of the LKB1 C-terminal domain promotes mesenchymal polarization and directional persistence during three-dimensional invasion by activating the Rho-GTPase RhoA in a kinase-independent manner. Conversely, LKB1 kinase activity represses FAK activity through MARK1, which subsequently inhibits downstream collagen remodeling during invasion.