Outlier detection identifies stable intra-chromosomal interactions over tens of million base pairs apart

A fundamental question in the regulation of mammalian genome expression patterns is how three-dimensional chromosome structures are coupled to dynamic transcriptional activity of specific genes. Our previous computational analyses of RNA-seq and Hi-C data revealed that functionally related genes that were coregulated by common transcription factors tended to be physically close (Zhang et al., PLoS Comp Biol, 15, e1006786 (2019)). Some genes well separated by their genomic distance along a chromosome were nevertheless in physical proximity in the context of three-dimensional chromosome structure. We developed an outlier detection procedure, and identified the existence of well-reserved long-range chromome-interaction structures (> 20 Mb) from hi-C data. To further verify these structures and examine whether they are transient or stable, we performed live-cell imaging of selected genomic loci labeled with the CRISPR-dCas9 system in human 293 T and A549 cells. We observed a pair of loci separated over 80 Mb to form a stable assembly that fluctuated together during hours of observations. Cells showed heterogeneity in the number of such assembled higher order structures. We hypothesize that this structural juxtapositioning may coordinate gene regulation through mechanisms like phase separation to create specific local chromosome environments (Zhang et al. Phys Rev. Lett., 112, 068101 (2014)), or canalize chromosome configuration space for cell type specification.