The spatial arrangement of interphase chromosomes in the nucleus is important 
for gene expression and genome function in animals and in plants. The recently 
developed Hi-C technology is an efficacious method to investigate genome 
packing. Here we present a detailed Hi-C map of the three-dimensional genome 
organization of the plant Arabidopsis thaliana. We find that local chromatin 
packing differs from the patterns seen in animals, with kilobasepair-sized 
segments that have much higher intrachromosome interaction rates than 
neighboring regions, representing a dominant local structural feature of genome 
conformation in A. thaliana. These regions, which appear as positive strips on 
two-dimensional representations of chromatin interaction, are enriched in 
epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 
insulator-like regions. Furthermore, although topologically associating domains 
(TADs), which are prominent in animals, are not an obvious feature of A. 
thaliana genome packing, we found more than 1000 regions that have properties of 
TAD boundaries, and a similar number of regions analogous to the interior of 
TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are 
each enriched for distinct epigenetic marks and are each correlated with 
different gene expression levels. We conclude that epigenetic modifications, 
gene density, and transcriptional activity combine to shape the local packing of 
the A. thaliana nuclear genome.