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Fig. 3 | Genome Biology

Fig. 3

From: Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana

Fig. 3

Transgene silencing by KNOT-linked silencing. a Seedlings growing on medium containing kanamycin show variable resistance (see also Additional file 1: Figure S3A). b Pearson’s correlation between phenotypic viability assessed by visual inspection (10—fully viable, 0—dead) in the presence of kanamycin and TIS interaction frequencies (IF) with KEEs and pericentromeres (see also Additional file 1: Table S3). c Pearson’s correlation between NPTII transgene expression and TIS interaction frequencies with KEEs and pericentromeres. d Pearson’s correlation between NPTII transgene expression and phenotypically assessed kanamycin resistance (see b). e Viability score (10—fully viable, 0—dead) of transgenic seedling populations (n = 30) grown on selective medium. Transgenic lines were selected by randomly choosing a homozygous SALK line (http://signal.salk.edu/cgi-bin/homozygotes.cgi) for each 300-kb genomic bin on Chr1. Numbers of transposons are indicated as a proxy for the presence of heterochromatin. Euchromatic and heterochromatic regions (purple and light red) correspond to chromatin states 1–7 and chromatin states 8–9, respectively, as previously defined [18] (see also Additional file 1: Table S4). f Pearson’s correlation analysis of interaction frequencies between the prospective TIS and the KNOT in the wild type and the viability score of transgenic lines with insertions at the respective TIS. TIS-KNOT interaction frequencies were calculated from Col-0 wild-type Hi-C matrices (100 kb bins) [5]

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