Quinodoz, S. A. et al. Cell https://doi.org/10.1016/j.cell.2018.05.024 (2018).
Great strides in understanding how eukaryotic genomes fold have been made with molecular methods based on cross-linking and ligation of genomic regions in close 3D proximity. But the need for ligation has also limited resolution and precluded regions that lie outside the ligation range from being incorporated into the overall structure. Quinodoz et al. have now found a way to profile higher-order interaction by using a method that does not rely on ligation. Their ‘split-pool recognition of interactions by tag extension’ (SPRITE) approach still requires cross-linking and fragmenting of chromatin. But instead of then ligating the ends, it splits the content in 96-well plates and barcodes molecules in each well. This process of pooling, splitting and barcoding is repeated several times, and eventually the string of barcodes for each fragment is read by sequencing. The barcode signature allows clustering of complexes that were part of a higher-order chromatin structure. SPRITE is not limited to pairwise interactions, and the researchers observed that active DNA regions in various A compartments interact and form higher-order complexes.