Figure 1.
Length distribution of H2Av nucleosomal DNA in heterochromatic and euchromatic regions.
A, Schematic of heterochromatic (black) and euchromatic (gray) regions of the Drosophila genome. B, Read length distribution of reads aligned to euchromatic and heterochromatic genomic regions, respectively. The Y-axis represents percentile of total mapped reads in euchromatin and heterochromatin, separately.
Figure 2.
Dinucleotide frequency distribution.
The dinucleotide count was calculated for both the forward and reverse strands, reading from the 5′ to 3′ direction. The frequency distribution of one dinucleotide (e.g. 5′-AC-3′) plotted at the top from left to right is equal to its complement (e.g. 5′-GT-3′) reported from right to left at the bottom. Self-complementary dinucleotides are reported on only one axis.
Figure 3.
Examples of detected H2Av locations in heterochromatic regions.
Three panels are shown, exemplifying different heterochromatic regions and at different zoom levels. The blue graph represents the number of forward strand reads mapped to each coordinate (and shifted 3′ to a higher coordinate by 73 bp to reflect the nucleosome midpoint). The red bar graph, scaled in the opposite direction, for comparison, represents the number of reverse strand reads mapped to each coordinate (shifted 3′ to a lower coordinate by 73 bp). Nucleosomes were predicted through GeneTrack using an exclusion zone of 147 bp and sigma of 20 bp [67], [68]. The blue and red hash marks indicate nucleosome midpoint positions. Two examples are shown.
Figure 4.
H2Av nucleosome density on chromosomes and organization at mRNA genes.
A, Weighted H2Av read counts were normalized to the amount of sequence present in each chromosomal region, and plotted. B, Nucleosomal DNA tag counts at each coordinates were plotted for both euchromatin and heterochromatin regions on the X chromosome. The height of blue bar indicates the total normalized tag count at each coordinate. Regions for euchromatin and heterochromatin is scaled differently along the X-axis. The Y-axis is on same scale. C, Euchromatin and heterochromatin genomes were divided into three categories: mRNA, other transcripts (tRNA, miRNA, transposons, etc), and non-coding regions. H2Av densities were calculated as total tag numbers divided by total base pair in all features in that particular category. D, Shown are a composite plots of the H2Av nucleosome occupancy distribution relative to TSSs (transcription start site, left panel) and TTSs (transcript termination site or polyA site, right panel) for the set of annotated heterochromatic and euchromatic genes. The number of genes included is indicated by N. Nucleosomal DNA read counts were weighted, binned, then normalized to the number of regions present in each bin, and plotted as a smoothed distribution. In order to represent a “pure” pattern, we removed those regions that were <300 bp from an adjacent TSS or TTS. Light gray-filled plot represents the distribution of reads in euchromatin. The black trace represents the distribution in heterochromatin.
Figure 5.
H2Av nucleosome organization at TIRE transposable elements.
A composite distribution of H2Av nucleosomal sequence tags is shown around the start (left panel) and end (right panel) of DNA TIR elements. Euchromatic elements are shown in the gray-filled plot and heterochromatic elements are indicated by the black trace. The relative location of TIR ends is shown as a black filled plot. The structure of the TIREs, drawn to approximate scale is shown above the plot. Multiple sequence alignments of TIREs is shown above the schematic, illustrating the proposed location of an H2Av nucleosome. Many TIREs are degenerate, lacking the internal homology regions to the transposon, and lacking a matching downstream inverted repeat.
Figure 6.
H2Av nucleosome organization flanking LTR and nonLTR retrotransposons.
A, Composite H2Av nucleosome occupancy distribution around the start (top left panel) or end (top right panel) of LTR elements. Euchromatic regions are plotted as gray fill, and heterochromatic regions as a black trace. N indicates the number of elements represented. The lower set of nine plots show the distribution of H2Av around the start of specific classes of LTRs. Numbers on the graph indicate the number of cases found, and are positioned closest to the trace it reflects. B, Composite H2Av nucleosome occupancy distribution around the start (left) or end (right) of non-LTR elements.