T-DNA-Genome junctions form early after infection and are influenced by the chromatin state of the host genome

Agrobacterium tumefaciens mediated t-dna integration is a common tool for plant genome manipulation. however,there is controversy regarding whether t-dna integration is biased towards genes or randomly distributed throughout the genome. in order to address this question,we performed high-throughput mapping of t-dna-genome junctions obtained in the absence of selection at several time points after infection. t-dna-genome junctions were detected as early as 6 hours post-infection. t-dna distribution was apparently uniform throughout the chromosomes,yet local biases toward at-rich motifs and t-dna border sequence micro-homology were detected. analysis of the epigenetic landscape of previously isolated sites of t-dna integration in kanamycin-selected transgenic plants showed an association with extremely low methylation and nucleosome occupancy. conversely,non-selected junctions from this study showed no correlation with methylation and had chromatin marks,such as high nucleosome occupancy and high h3k27me3,that correspond to three-dimensional-interacting heterochromatin islands embedded within euchromatin. such structures may play a role in capturing and silencing invading t-dna. © 2017 shilo et al.