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

Shay Shilo, Pooja Tripathi, Cathy Melamed-Bessudo, Oren Tzfadia, Theodore R Muth, Avraham A Levy

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish
JournalPLoS Genetics
Volume13
Issue number7
Pages (from-to)e1006875
ISSN1553-7404
DOIs
Publication statusPublished - Jul-2017

Keywords

  • Agrobacterium tumefaciens/genetics
  • Arabidopsis/genetics
  • Chromatin/genetics
  • DNA Methylation/genetics
  • DNA, Bacterial/genetics
  • Epigenomics
  • Euchromatin/genetics
  • Gene Transfer Techniques
  • Genome, Plant/genetics
  • Nucleosomes/genetics
  • Nucleotide Motifs/genetics
  • Plants, Genetically Modified/genetics

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