Fig. 9: Loss of NDX function causes rearrangement of chromatin organization.

a Circos plot representation of intra- and interchromosomal interactions that are significantly weakened (left) or enhanced (right) in ndx1–4 (p < 0.05, Slitherine pipeline). Color intensity of the arcs is proportional to the fold-change in interaction frequencies (ndx1–4/Col-0). Outer circle represents the five Arabidopsis chromosomes. Centromeres are highlighted in yellow. Knot engaged elements (KEEs) are shown in gray. b Knot interactions in the absence of NDX. Diagonal: five Arabidopsis chromosomes. Lower left triangle (below the diagonal): differential Hi-C matrix calculated from the ratio of ndx1–4 (red) and Col-0 (blue) interaction frequencies in Juicer. Resolution: 250 kb. Upper right triangle (above the diagonal): scheme of Knot interactions in the ndx1–4 mutant. Knot-associated regions (circles) and centromeres (squares) and are highlighted. The T-DNA insertion site inactivating the NDX locus (red line in chr4) also participate in forming an ectopic Knot interaction. Right panel: Proposed 3D model of the Knot in the ndx1–4 mutant. The structure involves de novo formation of inter-chromosomal contacts (highlighted in yellow). c, d Representative Knot contacts in ddm1-2, met1-3, clf28 swn7, and ndx1–4 mutants. Panel c shows de novo formed Knot contacts in the ddm1-2, met1-3, and ndx1–4 mutants that are missing from Col-0 and clf28 swn7. Panel d shows a ddm1-2 and met1-3 specific Knot contact that is missing from ndx1–4. e Pericentromeric chromatin shows local decompaction and enhanced interchromosomal interactions in the absence of NDX. Upper: Differential intra-centromeric Hi-C interactions represented by a pileup plot. Red and blue colors show enrichment or depletion of intrachromosomal interactions of centromeres in the ndx1–4 mutant. Diagonal bars show the exact locations of centromeric regions. Significantly different regions are shown below (identified by Slitherine; permutation test; p-value adjustment: Benjamini & Hochberg (FDR) method). Lower: The same as above but differential inter-centromeric interactions are shown. f Circos plot showing all intra- and interchromosomal interactions of centromeric regions that are significantly weakened or enhanced in the ndx1–4 mutant (p < 0.05, Slitherine pipeline). Color intensity of the arcs is proportional to the fold change in Hi-C interactions (ndx1–4/Col-0). Outer circle represents the chromosomes. Centromeres are highlighted in yellow.