Homological Coupling of Chromatin Fibers

We tested whether sequence homology exists between chromatin fibers at contact points using long-read chromatin conformation capture data. Analysis of 12 million PacBio CiFi reads from GM12878 cells yielded 6,055 accurately mapped ligation points. We developed a method to distinguish between ligation junctions in reads and genomic ligation points, excluding 20-50% of restriction sites that remained undigested due to protein protection. For each ligation point pair, we extracted 80kb genomic windows and measured sequence homology using MUMmer. We compared homology between actual pairs versus swapped control pairs. The analysis revealed an 8-fold enrichment of sequence homology at approximately 7 kb from the ligation points, with a 10 kb central depletion basin. This volcano-shaped profile showed that genomic regions brought together by chromatin folding have higher sequence homology than random region pairs. The central depletion basin likely arose because ligation point detection required initial alignment to a masked genome, creating bias against repetitive elements near the contact sites. Since transposable elements comprise over 50% of the genome and constitute the majority of homologous sequences, the observed enrichment of homology suggests that they may mediate chromatin contacts. We term this proposed mechanism homological coupling, where identical repetitive sequences could serve as anchors guiding chromatin folding.