T-DNA integration is rapid and 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 integration showed that selected events reported on previously were associated with extremely low methylation and nucleosome occupancy. Conversely, non-selected events from this study showed chromatin marks, such as high nucleosome occupancy and high H3K27me3 that correspond to 3D-interacting heterochromatin islands embedded within euchromatin. Such structures might play a role in capturing and silencing invading T-DNA.