1. Volume 10, Issue 2, Pages 340-344 (February 2017)
Influence of Chromatin 3D Organization on Structural Variations of the Arabidopsis thaliana Genome 
Jing-Fen Tao, Jin-Zhi Zhou, Ting Xie, Xiao-Tao Wang, Qing-Yong Yang, Hong-Yu Zhang 
Molecular Plant 
Volume 10, Issue 2, Pages (February 2017)
DOI: /j.molp
Copyright © 2017 The Author Terms and Conditions

2. Figure 1
Structural Variants (SVs) Exhibit an Obvious Bias toward the Regions with Higher Interchromosomal Interaction from Kilobase to Chromosome Size.
Three levels of structural variants (SVs) in the Arabidopsis genome, double-strand breakpoints (A–G), meiotic recombination (H), and complex combinations of rearrangements (I–K), generally tend to distribute in regions of higher interchromosomal interaction.
(A)–(C) The T-DNA insertion sites have an obvious bias toward higher interchromosomal interaction regions. Each violin represents the five different datasets (R1–R5; Supplemental Table 1) generated by multiple individual laboratories. The left green violin indicates the distribution of bins (50 kb) with T-DNA insertion sites, and the right blue violin indicates the distribution of bins without T-DNA insertion sites. The violins represent the density of values along the y-axis and are of equal area. The interchromosomal interaction (A) of bins with T-DNA insertion sites is higher than those without T-DNA insertion sites, whereas intrachromosomal interaction (B) exhibits the opposite trend, and the RI values (ratio of inter-to intrachromosomal interactions) were higher for regions with T-DNA insertions than for regions without T-DNA insertions (C). Significance is based on the Mann-Whitney U test; the complete results of the spatial position features analyses are presented in Supplemental Tables 3–5.
(D) A significant positive correlation was observed between the number of T-DNA insertion sites and RI values. Bins (50 kb) were classified into seven different groups depending on the number of T-DNA insertion sites. Each box group indicates a different T-DNA number as labeled on the x-axis, and different colors represent the five different datasets.
(E) The RI values of T-DNA insertion deserts (i.e., bins without T-DNA insertion sites) exhibit significant distance attenuation. The T-DNA insertion deserts were assigned as zero. The x-axis represents the distance between T-DNA insertion deserts and the nearest 20 bins with T-DNA insertions. The different colors indicate different experiments. The y-axis indicates the distribution of RI values for T-DNA insertion deserts and their immediate neighbor bins. The error bars represent the SE.
(F) Meiostic crossovers display a biased distribution. The crossover intervals in meiosis were classified as high (High Rec, brown), medium (Medium Rec, light green), and low (Low Rec, dark green) recombination intervals, according to the corresponding crossover frequency. The RI values (y-axis) of high recombination intervals were higher in different experiments (x-axis). The complete results of the statistical analyses are presented in Supplemental Table 6.
(G) Distributions of the frequency of unlinked ohnologs showing interchromosomal colocalization after complex combinations of rearrangements. The dot indicates the realistic data for 4431 ohnolog pairs, whereas the line depicts the distributions for 1 000 000 random experiments. The statistical significance is indicated. The complete results of the statistical analyses are presented in Supplemental Table 7.
(H) The retained ohnologs (green) after WGDs exhibit a higher interchromosomal interaction than non-ohnologs (blue). The complete results of the statistical analyses are presented in Supplemental Table 8.
(I)–(J) Illustration of the clustering distributions of DNA double-strand breaks (DSBs) and WGD-imprinted genes in the 1D and 3D genome. (I) Clustering distributions of DSBs (black arrow) and WGD-imprinted genes (red dots) in the 1D genome of Arabidopsis. (J) The DSBs and WGD-imprinted genes are not randomly distributed in the genome 3D space and tend to spread across the boundaries of local chromosome areas, which well explains the physical clustering of DSBs, ohnologs, and unlinked ancestrally neighboring genes, indicating that chromatin 3D organization have a significant impact on different types of SVs associated with DSBs or WGDs.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2017 The Author Terms and Conditions