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bioRxiv · 10.1101/2021.05.17.444465

Compartmap enables inference of higher-order chromatin structure in individual cells from scRNA-seq and scATAC-seq

Johnson, B. K.·Fortin, J.-P.·Hansen, K. D.·Shen, H.·Triche, T. J.
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Abstract

Single-cell profiling of chromatin structure remains a challenge due to cost, throughput, and resolution. We introduce compartmap to reconstruct higher-order chromatin domains in individual cells from transcriptomic (RNAseq) and epigenomic (ATACseq) assays. In cell lines and primary human samples, compartmap infers higher-order chromatin structure comparable to specialized chromatin capture methods, and identifies clinically relevant structural alterations in single cells. This provides a common lens to integrate transcriptional and epigenomic results, linking higher-order chromatin architecture to gene regulation and to clinically relevant phenotypes in individual cells.

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Johnson, B. K., Fortin, J.-P., Hansen, K. D., Shen, H., Triche, T. J.. 2021-05-18. Compartmap enables inference of higher-order chromatin structure in individual cells from scRNA-seq and scATAC-seq. https://doi.org/10.1101/2021.05.17.444465

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