Exploring The Influence Of Chromatin 3D Organization On Structural Variations Of The Arabidopsis Thaliana Genome

Genome variation is the material basis for biodiversity formation,development,disappearance,and species evolution,it consists of single nucleotide polymorphisms(SNP)and genomic structural variations(SVs).A larger fraction of genome is affected by SVs than SNPs,indicating that SVs may have more significant impacts or consequences for phenotypic variations(e.g.,various chronic diseases)and evolution than SNPs.Thus,SVs have received significant attention in human.However,little effort has been directed towards understanding the role of SVs in plants,especially the mechanisms underlying their occurrence and the evolutionary fixation remain poorly understood.Some research results indicated that chromatin 3D structure likely plays an important role in genome SVs,in order to verify this hypothesis in plants,we chose the genetic model plant Arabidopsis thaliana for a case study.In this study,we used five sets of published Arabidopsis thaliana high-quality chromatin interactions data and comprehensively examined the relationship between chromatin 3D structure and genome SVs at three different levels: exogenous T-DNA insertion mediated by Agrobacterium,endogenous crossover during meiosis,and largescale chromosomal rearrangements in the course of evolution by integrating the interaction and SVs data.The results show that the interaction ratio of inter-to intra-chromosomal interactions of 11,103 T-DNA insertion sites is relatively higher,a significant positive correlation was observed between the number of T-DNA insertion sites and the interaction ratio,and there is also correlation between the distance of T-DNA insertion sites and the interaction ratio(R = 0.869-0.906).For the 375 chromosomes fragments involved in meiosis,the interaction ratio of the sites with higher crossover frequency is higher.The retained gene pairs after whole-genome duplication events,4,431 ohnologs and 3,399 unlinked ancestrally neighbouring gene pairs have higher interchromosomal interaction,and the interaction ratio is higher than random gene pairs.In conclusion,Different levels of SVs in this study that driven by three different types of genetic events: exogenous,endogenous and species evolution and from kilobase,megabase to chromosome size scale are not randomly distributed in genomic 3D space but exhibit an obvious bias in the regions with higher interchromosomal interactions,that is the boundary of local chromosome territory.Combined with other researches,the result of this study fully demonstrates the influence of spatial organization of chromatin on structural variations.This study provides a theoretical basis and a new train of thought for further research on the underlying mechanisms responsible for the occurrence and existence of structural variations and the fate determination mechanisms after whole-genome duplication.It also further illustrates the importance of 3D genomics on the study of genome evolution.