Figure 1.

HCNE arrays are centrally positioned in large synteny blocks. (A) RA-HCNE sequence is enriched in large synteny blocks compared to RA-CDS. Dashed lines show the distributions when sequence not covered by any synteny block is excluded. (B) HCNE density, RA-CDS density, and synteny blocks on Dmel chromosome arm 2L. Synteny blocks (green boxes with black borders) are shown between the density curves and in the area under them. Density peaks were detected above a threshold (gray line) set to cover 80% of the area under the density curve for the chromosome arm. In the magnified section, HCNE density peaks are labeled with inferred regulatory target genes located in the same synteny block as the HCNE density peak. (C) Line histogram of position of density peaks within synteny blocks. For each density peak that was located within a synteny block, we computed the distance between the peak and the synteny break closest to it, and scaled the distances to [0, 0.5] by dividing with synteny block size. Dashed lines show distributions from 10,000 randomizations where synteny blocks were ordered independently of density peaks (Supplemental Fig. S3). (D) Histogram of median distance in each of the 10,000 randomizations. Arrows indicate medians for the nonrandomized data, and one-sided P-values indicate the fraction of randomizations having equal or more extreme medians.