Study Of Rice High Resolution Three-dimensional Genome Architecture And Transcription Regulation

The linear genome of eukaryotes folds and packs into a specific three-dimensional(3D)structure in the nucleus.The 3D genome is involved in a series of biological processes such as DNA replication,DNA repair,transcription regulation and plays crucial roles in cell differentiation,animal development and evolution.However,research on the 3D genome architecture of plants and its regulation of life processes is still in its infancy.As a monocotyledonous plant,rice feeds nearly half of the world's population.It is of great scientific significance to reveal the three-dimensional genome structure of rice and its mechanism of regulating gene transcription.In recent years,using Hi-C technology,scientists have made many important discoveries in rice 3D genome research and identified some large structural units such as compartment and topologically associtated domains(TADs).However,limited by factors such as low resolution,it is difficult to accurately detect the fine 3D genome structure of chromatin loops such as gene promoter-promoter interaction(PPI)via Hi-C method.In this study,a Long-read Ch IA-PET technology was used to construct a chromatin interaction map of heterochromatin Interaction mediated by H3K9me2 in Zhenshan 97(ZS97)and chromatin interaction map of active genes mediated by RNA polymerase II(RNAPII)and H3K4me3.By integrating the rice's epigenomic data,transcriptome data,genetic variation data,the characteristics of rice 3D genome structure and the effects of genetic variation on the 3D genome structure and gene expression regulation of rice were revealed.The research results are as follows:(1)A single-gene resolution 3D genome map of rice was constructed that could detect chromatin loops.H3K9me2 modified region(heterochromatin)participated in 12,517 chromatin interactions,while H3K4me3 modified region(promoter)participated in 12,887 chromatin interactions and RNAPII mediated 26,570 chromatin interactions. Heterochromatin interactions are mainly located in the periphery of the centromere,while H3K4me3 and RNAPII associated chromatin interactions are mainly located on the chromosome arms.(2)By integrating epigenomic and transcriptome data,the basic characteristics of the three interactions are systematically analyzed.Compared with the H3K9me2 modified gene that does not participate in heterochromatin interaction,the expression level of the H3K9me2 modified gene involved in the interaction is not significantly different,as both of them is very low.H3K9me2 binding site with a higher TE density and a wider peak is more likely to participate in heterochromatin interactions.For interactions involving active genes,compared to Basal Promoter genes that are not involved in the interaction,the anchor genes involved in the interaction are almost housekeeping genes,with a higher percentage of rice germplasm core genes and higher expression levels.Strikingly,these interactive anchor genes tend to be co-expressed.(3)Compartment model was presentd to depict the rice 3D genome,which was divided into five chromatin interaction domains(CIDs)with different transcription potentials,termed as AID(active module),HID and gap(inactive / weak transcription module),MID(active module,conversion module between AID and HID),and TID(medium transcription module).These CIDs are finer structures than topologically assocaited domains(TADs)and are similar to sub-TADs.The difference of transcriptional activity in different CIDs depends on the proportion of anchoring genes involved in active chromatin loop formation.These modules are distributed on the rice chromosome,covering 84% of the rice genome,and are organized into relatively independent transcriptional space with different biological functions.(4)Based on genetic variation data between two rice varieties,ZS97 and MH63,the effects of genetic variation on rice chromatin topological structure and gene transcription regulation were revealed.(5)A three-dimensional genome microscopic imaging system for rice was established.The three-dimensional immunofluorescence(3D-IF)and improved fluorescence in situ hybridization(HCR-FISH)experiments were used to verify the existence of high-frequency chromatin interactions and interacting domains in rice nuclei.