Fig. 1

Chrom3D integrates Hi-C and nuclear lamin ChIP-seq data to provide an ensemble of 3D genome structures with radial positioning information of loci. a Chrom3D principles. Hi-C and lamin ChIP-seq data are combined to define beads (TADs) subjected to interaction constraints between them, based on Hi-C data, or to interaction constraints with the NP, based on LMNA ChIP-seq data (LADs). Hi-C and LAD maps shown are dummies for explanation purposes. Additional file 1: Figure S2 shows an actual representation of the relationship between TADs and LADs. During a simulation, TADs are rearranged with a modeled nucleus by a chromosome move (orange arrow) selected among a set of five possibilities (Additional file 1: Table S1) in order to juxtapose two interacting TADs (red beads), and position a LMNA-associated TAD at the NP (blue bead). Radius of the modeled nuclei is 5 μm. b Loss-score values and representative structures during a simulation; each chromosome is colored differently. c Example of a Chrom3D whole-genome 3D structure; chromosomes are distinctively colored. d Tomographic views of the structure in (c), showing LMNA-associated TADs (blue beads), all interacting TAD pairs (red beads), and interacting TAD pairs in which at least one TAD is associated with LMNA (purple “merged” beads). Gray beads visualize all other TADs. e Percentage of TADs at the NP as a function of Hi-C and LMNA constraints across 400 structures; **P < 2.2 × 10^–16; *P = 8.53 × 10^–5 (Mann–Whitney U tests)