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T-DNA integration is rapid and influenced by the chromatin state of the host genome

Shay Shilo, Pooja Tripathi, Cathy Melamed-Bessudo, Oren Tzfadia, Theodore R. Muth, Avraham A. Levy
doi: https://doi.org/10.1101/104372
Shay Shilo
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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Pooja Tripathi
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, IsraelDepartment of Plant Pathology Volcani Center-ARO P.O.Box 6 Bet-Dagan 50250 ISRAEL
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Cathy Melamed-Bessudo
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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Oren Tzfadia
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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Theodore R. Muth
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, IsraelCUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA.
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  • For correspondence: tmuth@brooklyn.cuny.edu avi.levy@weizmann.ac.il
Avraham A. Levy
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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  • For correspondence: tmuth@brooklyn.cuny.edu avi.levy@weizmann.ac.il
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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 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.

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Posted January 31, 2017.
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T-DNA integration is rapid and influenced by the chromatin state of the host genome
Shay Shilo, Pooja Tripathi, Cathy Melamed-Bessudo, Oren Tzfadia, Theodore R. Muth, Avraham A. Levy
bioRxiv 104372; doi: https://doi.org/10.1101/104372
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T-DNA integration is rapid and influenced by the chromatin state of the host genome
Shay Shilo, Pooja Tripathi, Cathy Melamed-Bessudo, Oren Tzfadia, Theodore R. Muth, Avraham A. Levy
bioRxiv 104372; doi: https://doi.org/10.1101/104372

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