| Plant cell differentiation requires changes in the transcriptional regulatory network of multiple genes,including those encoding transcription factors.There is increasing evidence that epigenetic reprogramming affects the expression of differentiation-related genes during plant cell differentiation.Cotton fiber is a highly differentiated single-cell structure initiated from the ovule epidermis,and its differentiation and development process is divided into four relatively differential but overlapping stages: initial,elongation,secondary cell wall synthesis,and dehydration maturation.Therefore,cotton fibers can be used as a model system for studying plant cell differentiation.During these four periods,the morphological and structural changes of fiber cells were accompanied by changes in important physiological and biochemical processes,among which a large number of genes were involved in the regulation of fiber development.Previous studies by our group have illustrated the evolutionary reorganization of higher-order chromatin structure in cotton leaves after polyploidization and differential amplification of transposable elements(TEs),but the understanding of the 3D chromatin organization of cotton fiber and their functional significance remains limited.In this study,the signal-to-noise ratio of the Hi-C experimental data was greatly improved by improving the in situ Hi-C technique.We performed dynamic 3D genomics studies of cotton fiber using G.barbadense cv.3-79,aiming to dissect the relationship between chromatin topology changes and gene transcriptional regulation during fiber development.The relevant research results are as follows:(1)During fiber development,the total number of expressed genes gradually decreased,accompanied by a decrease in active histone modifications of H3K27 ac and H3K4me3 and an increase in repressive histone modifications of H3K9me2.During fiber development,it is not genes in a single subgenome that promote fiber development,but the relay of homologous genes in different subgenomes to promote fiber development.(2)We have constructed a chromatin interaction matrix with a resolution of 5 Kb.At different resolutions,different higher-order chromatin structures emerged.During fiber development,intrachromosomal interactions decrease and interchromosomal interactions increase.The dynamic three-dimensional genome structure we have established can provide a resource for uncovering higher-order chromatin structure and transcriptional regulation during fiber development.(3)We used a 40 Kb Hi-C matrix to separate the chromatin into A and B compartments at each developmental stage.During fiber development,there is a dynamic switch between A/B compartments,which facilitates the transition of more genes from A to B compartments.The expression levels of genes in the A/B switching region also changed correspondingly,indicating that large-scale 3D structure changes are related to gene expression.At the compartmental level,the At and Dt subgenomes act synergistically throughout fiber development.(4)We have identified a total of 10571 TAD-like structures covering 83.53% of the genome by using the 20 kb resolution matrix.Conserved TAD-like structure boundaries are more insulating than dynamic TAD-like structure boundaries.The expression levels of genes at the boundaries of TAD-like structures were higher than those of genes inside TADlike structures.TE insertion/elimination is associated with the switching of subgenomespecific boundaries,resulting in a partition/fusion of TAD-like structures between the two subgenomes.Homologous genes with expression bias are preferentially located in regions where the spatial location of TAD-like structures changes.(5)TAD-like structure cliques constitute higher-order chromatin aggregates and represent larger-scale chromatin structures involved in transcriptional regulation.During fiber development,many active cliques dissociate;in the later stage of fiber development,the dynamic changes of cliques are more obvious than in the earlier stage.TAD-like structure interactions represented by cliques preferentially occur in the B compartment and are accompanied by the silencing of development-related genes in cotton fiber.(6)We have identified a total of 764188 chromatin loops using the 5 Kb resolution matrix,most of which are stage-specific.And as fibers develop,many chromatin interactions in active genomic regions are lost.The deposition of inactive modifications and the removal of active modifications may explain why more G-N loops at later stages of development are associated with lower expression levels of these loop-related genes.We constructed a subgenomic chromatin interaction network using HG-HG loops,and found that the interaction network of the At subgenome was quite different from that of the Dt subgenome.In conclusion,our study constructed a high-resolution dynamic three-dimensional genome map of cotton fibers for the first time,revealing the topological basis of subgenome cooperative regulation of allotetraploid cotton fiber development at the level of chromatin high-level structures such as chromosome territory,chromatin compartments,TAD-like structures and chromatin loops,which has important implications for cotton functional genome and developmental biology research. |
