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Improving chromatin-interaction prediction using single-cell open-chromatin profile and making insight about the cis-regulatory landscape of the human brain

Single-cell open-chromatin profiles have the potential to reveal the pattern of chromatin-interaction in a cell-type. However, currently available cis-regulatory network prediction methods using single-cell open-chromatin profiles focus more on local chromatin-interactions despite the fact that long-range interaction among genomic sites plays a significant role in gene regulation. Here, we propose a method that predicts both local and long-range interactions among genomic sites using single-cell open chromatin profiles. Using our method’s better sensitivity, we could predict almost 0.7 million interactions among genomic sites across 7 cell-types in the human brain. The chromatin-interactions estimated in the human brain revealed surprising but useful insight about target genes of human-accelerated-elements and disease-associated mutations.