Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions

Meiotic recombination and chromatin variation between A. thaliana transposons. (A) Pie chart showing A. thaliana transposon families, with slice size proportional to physical length, and color-coded according to SPO11-1-oligo (Z-score standardized log₂[SPO11-1-oligos/gDNA]) levels. Inset colored boxes are shaded equivalent to the genome-wide mean (purple), minimum (blue), and maximum (red) values. (B) As for A, but analyzing nucleosome occupancy (Z-score standardized log₂[MNase/gDNA]). (C) Box plots showing SPO11-1-oligo and nucleosome occupancy, according to transposon SPO11-1-oligo hexile groups, with horizontal lines indicating the genome average value. Inset pie charts show the proportion of DNA (red) and RNA (blue) transposons for each SPO11-1-oligo transposon hexile. (D) Density of transposons through the A. thaliana genome according to SPO11-1-oligo hexile: (red) highest; (blue) lowest. x-Axis ticks indicate NBS-LRR gene homolog positions. Plotted beneath are SPO11-1-oligos (red) versus the density of Helitron/Pogo/Tc1/Mariner class DNA transposons (blue), or Gypsy RNA transposons (blue).