Figure 3.—

Genes situated in proximal heterochromatin require roX RNA for full expression in males. (A) Genes in proximal heterochromatin have reduced expression in roX1^SMC17AroX2 male larvae. Box plots were generated using the log₂ expression ratios (mutant/control) presented in Figure 1A. The mean expression of genes in proximal heterochromatin on the second and third chromosomes decreases by 0.17 in roX1^SMC17AroX2 males (adjusted P-value of 0.003). The mean expression of X-linked genes decreases by 0.24, and expression of fourth-linked genes decreases by 0.58. Changes of the X and fourth chromosome have an adjusted P-value of <6.6 × 10⁻¹⁶. Only genes present in at least 2 out of 3 arrays contributed to this analysis (8347 in second and third euchromatin; 1533 in X euchromatin, 73 in second and third heterochromatin, and 74 on the fourth chromosome). (B) Fourth-linked and heterochromatic genes do not require roX RNA for full expression in females. Box plots were generated using the log₂ expression ratios (mutant/control) presented in Figure 1C. The mean change in expression of X-linked genes in roX1^SMC17AroX2 females is −0.04. Second and third chromosome heterochromatic genes and fourth- linked genes have a slight average increase (0.06 and 0.01, respectively) that is not statistically significant. Only genes present in at least 2 out of 3 arrays contributed to this analysis (7097 in second and third euchromatin, 1336 in X euchromatin, 57 in second and third heterochromatin, and 69 on the fourth chromosome). Enrichment for heterochromatic genes is described in File S1.