Chromatin Architectural Alterations Associate With Responsive Transcriptional And Epigenetic Variations Due To Mutation Of A Major CG Methytransferase OsMET1-2 In Rice

Hierarchical 3D chromatin architectures have been extensively characterized by Hi-C(High-throughput Chromosome Conformation Capture)technique in different eukaryotic species.The association between chromatin architectural features and epigenetic modifications has been well-established in animals.However,the potential impact of DNA methylation on chromatin architecture is understudied in plants,and available studies are confined to the model plant Arabidopsis thaliana.Because plant species differ in genome size,composition,and overall chromatin packing,it is unclear to what extent findings from A.thaliana will hold in other species.Moreover,the incomplete profiles of chromatin architecture and the still low-resolution of Hi-C data from A.thaliana have hampered the characterization of subtle chromatin structures and their specific associations with DNA methylation.Here,we used a genome-wide Hi-C method to construct a high-resolution interaction map for the null Os MET1-2(gene of a major CG methylase)mutant of rice(osmet1-2 mutant)and its isogenic wild-type(cv.Nipponbare).We show that compared with WT,significant changes in hierarchical chromatin structures occurred due to genome-wide loss of CG methylation in osmet1-2 mutant.The changes include intra-and inter-chromosomal interaction,A/B compartment transition,and TAD reprogramming.Moreover,utilizing the published and self-generated transcriptional(m RNA and lncRNA)and epigenetic(DNA methylome and representative active and silencing markers)data,we also interrogated the potential relationship between 3D chromatin interaction and transcription and epigenetic modifications.Our findings also provide novel insights into the potential function of CHH methylation and local intergenic long non-coding RNA(lincRNA)expression in TAD formation in rice.By comparing the null At MET1 mutant of A.thaliana(atmet1)and its wild type(Col-0),we confirmed that DNA methylation plays a similar essential role in hierarchical chromatin packing in A.thaliana and rice.In this study,we not only performed Hi-C in the null mutation of a critical CG methylase to construct the first high-resolution interaction map,but also sheded the impact of CG methylation on 3D chromosomal conformation from a wider perspective.This study provides novel insights into the mechanism of TAD formation in plants,as well as the theoretical basis for the study of functional genomics and rice improvement.