Fig. 1

Chromosome packing in interphase nuclei of Arabidopsis thaliana seedlings. a A genome-wide interaction map of A. thaliana seedlings at 20-kb resolution. The normalized contact strength is shown with color gradient. For all chromosomes, the intra-chromosomal contact decreases as a function of genomic distance. Arrows highlight selected features. (i) The centromeric and pericentromeric regions are tightly packed and have few interactions with regions located on chromosome arms. This corresponds to general observations that centromeric regions appear as bright dots in A. thaliana nuclei stained with DAPI (4′6-diamidino-2-phenylindole dihydrochloride). On the other hand, in Hi-C maps of mutant plants where heterochromatin is decondensed, such as met1, ddm1, suvh4, suvh5 suvh6, and atmorc6, pericentromeric regions interact less with each other and more with the chromosome arms [32, 39]. (ii) Telomeres from different chromosomes are close to each other. According to fluorescent in situ hybridization (FISH) studies, telomeres often gather around the nucleolus [4]. (iii) Strong interaction among a subset of interstitial heterochromatin regions. These interactions have been captured by four independent Hi-C experiments [32–34, 39]; some of these interactions have also been seen with FISH [32, 33]. This Hi-C map is reproduced from our previously published interaction matrix [34]. b Diagram summarizing the conformation of interphase A. thaliana chromosomes with packing inferred from cytological and Hi-C experiments. Further details are shown for chromosomes 3 and 4. Every chromosome occupies a distinct territory (five differently colored territories are shown in this nucleus cross-section), but the relative positioning of the chromosomes within nuclei is largely random [59]. The tightly packed centromeric/pericentromeric portion (chromocenter) of every chromosome is often located close to the nuclear periphery or the nucleolus [4]. Chromocenters can fuse randomly, which produces strong inter-chromosomal interactions on the Hi-C map. Telomeres often cluster around the nucleolus, except for those close to nucleolus-organizing regions (NORs) on chromosomes 2 and 4 (not shown in this diagram), which frequently associate with their respective chromocenters [4]. The interactive heterochromatic island (IHI)/KNOT engaged element (KEE) regions form strong intra-chromosomal, and sometimes inter-chromosomal contacts (not shown in this diagram), and are readily spotted on Hi-C maps