An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?

Abstract

Background: X chromosomes are subject to dosage compensation in Drosophila males. Dosage compensation requires cis sequence features of the X chromosome that are present in both sexes by definition and trans acting factors that target chromatin modifying machinery to the X specifically in males. The evolution of this system could result in neutral X chromatin changes that will be apparent in females.

Results: We find that the general chromatin structure of female X chromosomes is distinct from autosomes. Additionally, specific histone marks associated with dosage compensation and active chromatin marks on the male X chromosome are also enriched on the X chromosomes of females, albeit to a lesser degree.

Conclusions: Our data indicate that X chromatin structure is fundamentally different from autosome structure in both sexes. We suggest that the differences between the X chromosomes and autosomes in females are a consequence of mechanisms that have evolved to ensure sufficient X chromosome expression in the soma of males.

Figure 1

Sheared chromatin DNA-Seq coverage in male and female adult flies. (A-B) Box plots of the distributions of average DNA-Seq sequence coverage (in non-overlapping 1 kb windows) in male (A) and female (B) adult flies separated by chromosome arms (X chromosome in red). 25th to 75th percentiles (boxes), medians (lines in boxes), and ranges (whiskers, 1.5 times the interquartile range extended from both end of the box ) are indicated for each chromosome. Significance of the chromosome arm distributions relative to the whole genome data set as determined by permutation sampling and KS test (C, D).

Figure 2

DNA-Seq coverage profiles of X chromosome and autosome gene features. (A-H) The average sequence coverage profiles of exon/intron regions and regions near transcription start sites (TSS) and termination sites (TTS) of all annotated gene models on the X chromosome (red), major autosomes (black), and the dot chromosome 4 (blue) in male (A-D) and female (E-H) adult flies. Male X chromosome coverage was multiplied by two to correct for karyotype. Significance of the chromosome arm distributions relative to the whole genome data set as determined by permutation sampling and KS test for females (I-L). P Values < 10^-15 are off-scale (black arrow).

Figure 3

Histone mark distributions. Box plots of ChIP input DNA intensities (log₂) (A), H4K16ac ChIP/input ratios (log₂) (B), H3S10ph ChIP/input ratios (C) and H3K4me2 ChIP/input ratios (D) in male (left) and female (right) adult flies separated by chromosome arms (X chromosome in red). See Figure 1 for box plot format. (E-J) The distributions of ChIP/input ratios for chromosome arms were compared inter se. Box plots of Bonferroni corrected P values from KS tests of ChIP/input ratios in all ChIP-chip replicates in male (E-G) and female (H-J) adult flies are shown. See Figure 1 for box plot format. P Values < 10^-15 are off-scale (red arrow).

Figure 4

Correlation among histone marks. K-means clustering (k = 2) of rank orders for ChIP enriched DNA/input ratios of individual histone marks in male and female adult flies. X chromosome genes (top) and autosome genes (bottom) are clustered separately. The order of ChIP samples was fixed as indicated in the figure. Genes enriched for histone marks (yellow) and genes depleted for histone marks (blue) are indicated.

Figure 5

Correlation between marks and expression. Box plots of expression intensities (log₂) of male or female adult flies for genes enriched for H4K16ac (A), H3S10ph (B), H3K4me2 (C) (ChIP/input percentile rank >90%) and genes depleted for those three histone marks (ChIP/input percentile rank <10%) in male or female adult flies. See Figure 1 for box plot format. Significance differences (P < 10^-2, Bonferroni corrected KS test) between genes enriched and depleted for histone marks are indicated (asterisks).

Figure 6

H4K16ac enrichment and sex-biased expression. (A) Average H4K16ac ChIP/input ratios (log₂) in male flies for genes showing male-biased expression (blue) and non-biased expression (grey) in whole flies and in the soma. (B) Average H4K16ac ChIP/input ratio (log₂) in female flies for genes showing female-biased expression (red) and non-biased expression (grey) in whole flies and in the soma. Significance differences (P < 10^-2, Bonferroni corrected KS test) between genes with sex-biased expression and genes with non-biased expression are indicated (asterisks).

Figure 7

Model of sex chromosome chromatin structure evolution.