Three-dimensional Genome And Transcriptome Analysis Of Deinococcus Radiodurans

Ultraviolet radiation can damage DNA,produce pyrimidine dimers,and even kill cells.Deinococcus radiodurans has a complex damage repair pathway and is surprisingly resistant to ultraviolet radiation.But so far,the understanding of how it resists UV irradiation is very limited.In this work,Chromosome Conformation Capture and Sequencing(3C-seq)and RNA-seq techonologies were used to determine the three-dimensional genomic and transcriptomic data of D.radiodurans R1 strain under normal culture and 750 J/m~2 UV irradiation conditions.By analyzing the chromosome interaction matrix and differentially expressed genes(DEGs),the structure and function of the chromosomes before and after UV irradiation were compared.First,chromosome interaction matrixes with 5 kb resolution under normal culture and irradiation conditions were constructed and heat maps were generated.The results showed that:chromosomeⅠdisplays a significant main diagonal and a less obvious secondary diagonal,indicating that the two homologous arms of chromosomeⅠwere close to each other.ChromosomeⅡonly has an obvious main diagonal,indicating that the two homologous arms of chromosomeⅡare far away from each other,and the main diagonal is divided into two parts.Among them,the former part interacts more frequently with chromosomeⅠ,and the latter part interacts more frequently with the large plasmid pMP1.Then,the EVRC software was used to model the multi-chromosome structure.The results showed that the three-dimensional structure of chromosomeⅠwas ship-shaped,and the origin of replication oriC1 was located at the prow,while the structure of chromosomeⅡwas more like a ring.Then,the location and number of chromosomal interaction domains(CIDs)and their boundaries were determined by directionality index analysis,and it was found that there were usually long genes with high expression at the CIDs boundaries.By analyzing the ratio diagram of interaction matrix and scalogram,it was found that the short-distance interaction of D.radiodurans chromosomes was reduced and the structure became loose under 750 J/m~2 UV irradiation compared with normal culture condition.Transcriptome differential expression profile analysis showed that the key genes in the damage repair pathways were significantly upregulated in response to UV irradiation,including non-homologous end joining(NHEJ),single-strand annealing(SSA),nucleotide excision repair(NER),mismatch repair system(MMR).Functional enrichment analysis was performed on CIDs boundary genes,the genes in different chromosome structure regions and transcriptome DEGs before and after irradiation.Comprehensive results showed that translation-related functions(such as amino acid synthesis,ribosome assembly,ABC transport,etc.)and ATP-binding related functions became active after irradiation.Functions associated with redox reactions(such as redox enzyme activity,ubiquinone,cytochrome,heme,propionic acid metabolism,etc.)are inhibited.The present work is the first three-dimensional genomic study of D.radiodurans,which contributes to the understanding of the molecular mechanism of extreme resistance of this species from the perspective of chromosome 3D structure.