Abstract
The formation of polyploids significantly increases the complexity of
transcriptional regulation, which is expected to be reflected in sophisticated
higher-order chromatin structures. However, knowledge of three-dimensional (3D)
genome structure and its dynamics during polyploidization remains poor. Here,
we characterize 3D genome architectures for diploid and tetraploid cotton, and
find the existence of A/B compartments and topologically associated domains
(TADs). By comparing each subgenome in tetraploids with its extant diploid
progenitor, we find that genome allopolyploidization has contributed to the
switching of A/B compartments and the reorganization of TADs in both
subgenomes. We also show that the formation of TAD boundaries during
polyploidization preferentially occurs in open chromatin, coinciding with the
deposition of active chromatin modification. Furthermore, analysis of
inter-subgenomic chromatin interactions has revealed the spatial proximity of
homoeologous genes, possibly associated with their coordinated expression. This
study advances our understanding of chromatin organization in plants and sheds
new light on the relationship between 3D genome evolution and transcriptional
regulation.
doi:10.1038/s41477-017-0096-3 IF=10.08