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

(2017) PLOS GENETICS. 13(7).
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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.
Keywords
STRAND BREAK REPAIR, ARABIDOPSIS GENOME, TRANSGENE EXPRESSION, INSERTION, SITES, WIDE ANALYSIS, PLANT GENOME, INTEGRATION, RECOMBINATION, SEQUENCES, GENES

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Chicago
Shilo, Shay, Pooja Tripathi, Cathy Melamed-Bessudo, Oren Tzfadia, Theodore R Muth, and Avraham A Levy. 2017. “T-DNA-Genome Junctions Form Early After Infection and Are Influenced by the Chromatin State of the Host Genome.” Plos Genetics 13 (7).
APA
Shilo, S., Tripathi, P., Melamed-Bessudo, C., Tzfadia, O., Muth, T. R., & Levy, A. A. (2017). T-DNA-Genome junctions form early after infection and are influenced by the chromatin state of the host genome. PLOS GENETICS, 13(7).
Vancouver
1.
Shilo S, Tripathi P, Melamed-Bessudo C, Tzfadia O, Muth TR, Levy AA. T-DNA-Genome junctions form early after infection and are influenced by the chromatin state of the host genome. PLOS GENETICS. 2017;13(7).
MLA
Shilo, Shay et al. “T-DNA-Genome Junctions Form Early After Infection and Are Influenced by the Chromatin State of the Host Genome.” PLOS GENETICS 13.7 (2017): n. pag. Print.
@article{8530018,
  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.},
  articleno    = {e1006875},
  author       = {Shilo, Shay and Tripathi, Pooja and Melamed-Bessudo, Cathy and Tzfadia, Oren and Muth, Theodore R and Levy, Avraham A},
  issn         = {1553-7404},
  journal      = {PLOS GENETICS},
  keywords     = {STRAND BREAK REPAIR,ARABIDOPSIS GENOME,TRANSGENE EXPRESSION,INSERTION,SITES,WIDE ANALYSIS,PLANT GENOME,INTEGRATION,RECOMBINATION,SEQUENCES,GENES},
  language     = {eng},
  number       = {7},
  pages        = {16},
  title        = {T-DNA-Genome junctions form early after infection and are influenced by the chromatin state of the host genome},
  url          = {http://dx.doi.org/10.1371/journal.pgen.1006875},
  volume       = {13},
  year         = {2017},
}

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