The epigenetic landscapes of genes define their transcriptional activity. Multiple epigenetic marks crosstalk with each other and consequently shape cell fate in development and disease. We have developed a multi-omics assay that jointly measures chromatin accessibility, DNA methylation and 3D genome organization on the /same/ DNA molecule. Combined with third-generation sequencing, this approach preserves higher-order concatemers and thus enables us to capture multi-way chromatin contacts in addition to pairwise contacts. However, current software typically addresses either long-read epigenomics or concatemer-based 3D genome analysis, and no comprehensive solution exists for an integrated interpretation of these readouts at single-molecule resolution. We therefore aim to develop a modular toolbox that addresses all modalities of multi-omics long read information. The toolbox is designed to analyze the full assay output within one workflow and includes reference-based deconvolution for mixed samples, enabling haplotype-aware assignment of molecules and cell-type deconvolution from informative loci. By unifying single-molecule epigenetic and 3D genome analysis, our framework enables systematic characterization of epigenetic states together with their spatial context. This work provides a computational foundation for studying allele-specific regulation, cellular heterogeneity and genome organization from native long-read multi-omics data.

Co-authors: Henrik Köppke, Scott Lacadie, Roseen Musallam, Uwe Ohler