Genome-wide profiling of H3.3 in Arabidopsis . (A) H3.3-YFP is targeted to the nucleus. Confocal images of nuclei from Arabidopsis roots showing H3.3-YFP (green) and a DNA-counterstain with DRAQ5 (red). Open arrowheads mark heterochromatic chromocenters. Scale bars: 2 μm. (B) Genome-wide profiles of H3.3 enrichment (red), transposable element (TE; yellow) and gene density (green). Bars mark centromeric and pericentric heterochromatin. (C) Nucleosome positions were detected by fitting the smoothed ChIP-chip signal (black line with squares) to a parabola model (green dashed line). The position of the maximum of each fitted parabola peak was regarded as the center of a nucleosome (cross). (D) Deconvolution of H3.3 enrichment at positions of nucleosomes (black) into a background (green) and a specific (blue) component using a mixture model. The red area indicates nucleosomes that have higher than 75% probability belonging to the specific component. (E) Comparison of observed and expected distribution of H3.3 nucleosomes across different genomic features (that is, protein coding gene, pseudogene, transposable element gene, transposable element, microRNA (miRNA), tRNA, non-coding RNA (ncRNA)).