Abstract: Methods for analyzing spatial proximity and epigenetic profile of nucleic acids in cells, the method comprising: fragmenting the nucleic acids, the fragmented nucleic acids comprising overhanging ends; filling in the overhanding ends with one or more labeled nucleotides; joining the filled in ends to create one or more end-joined nucleic acid fragments with one or more junctions; treating the end-joined nucleic acid fragments with bisulfite; isolating the bisulfite-treated end-joined nucleic acid fragments using the label; and determining sequence at the one or more junctions in the bisulfite treated end-joined nucleic acid fragments, thereby determining spatial proximity between the nucleic acids and the methylation profile of the nucleic acids.

Abstract: Embodiments provide a method for sequencing and assembling long DNA genomes comprising generating a 3D contact map of chromatin loop structures in a target genome, the 3D contact map of chromatin loop structures defining spatial proximity relationships between genomic loci in the genome, and deriving a linear genomic nucleic acid sequence from the 3D map of chromatin loop structures