Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds

Abstract

We compared global patterns of gene expression between two bird species, the chicken and zebra finch, with regard to sex bias of autosomal versus Z chromosome genes, dosage compensation, and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the noncoding RNA MHM (male hypermethylated) and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male-to-female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. This study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows other differences in sex bias. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.

Figure 1.

(A) Distributions of log₂ male-to-female (M:F) ratios of gene expression ratios for zebra finch telencephalon at four ages. Autosomal (A) genes (solid line) have a distribution around a mode of 1 (log₂ ratio of 0), showing that average autosomal genes are not sex-biased. The width of the distribution is a measure of overall sex bias, which is smallest in adulthood. In contrast, the distribution for Z genes (dotted line) is shifted significantly to the right, indicating that there is an overall male bias of Z genes. Nevertheless, some Z genes show no sex bias, indicating that some process compensates for the sex difference in Z copy number for those genes. Bin size = 0.1. (B) Z:A ratios of expression for each individual zebra finch (left), compared to published values for chicken embryo (Itoh et al. 2007). In general, Z:A ratios were comparable in the two species, with values in male near 1 and values in females near 0.8.

Figure 2.

Sex bias in gene expression along the zebra finch Z chromosome. (A) Plot of M:F ratios of expression ratios of individual Z genes as a function of Z chromosome gene position using data from day 45 zebra finch telencephalon. (B) Graph of the running average of 30 M:F ratios of expression (data from A) plotted at the median gene position along the zebra finch Z chromosome.

Figure 3.

Alignment of the chicken genome sequence near the MHM locus (27.8–28.1 Mb) on Zp, with the corresponding zebra finch genome sequence at 64.0–64.3 Mb on Zq. The region encoding the MHM non-coding RNA is not present in the current draft of the zebra finch genome.

Figure 4.

(A) Colocalization in interphase chicken fibroblasts of the MHM RNA and histone 4 acetylated at lysine 16. (Left) DAPI-stained nuclei. (Second panel from left, green) RNA FISH showing the accumulation of MHM RNA near the MHM locus in females only. (Third panel from left, red) The accumulation of H4K16Ac at the same location. (B) The H4K16Ac staining of zebra finch cells does not have any specific pattern of signal accumulation. DNA was DAPI-counterstained. The signal strength of H4K16Ac staining in chicken (A) and zebra finch (B) is not comparable; the H4K16Ac signal in zebra finch was overexposed to illustrate the absence of even weak signal.

Figure 5.

Scatterplot showing M:F ratios of gene expression in zebra finch and chicken for autosomal (A) (red) and Z genes (green). M:F ratios were compared in zebra finch telencephalon in day 45 versus adult samples (A), in chicken embryonic brain versus zebra finch adult brain (B), and in chicken embryonic heart versus brain samples (C). Within species (A,C), M:F ratios were more correlated for Z genes than for A genes. Between species (B), Z gene M:F ratios were only weakly correlated, and A gene M:F ratios were uncorrelated. Correlation coefficients were: (A) Z genes, r = 0.91; A genes, r = 0.35; (B) Z genes, r = 0.16; A genes, r = 0.05; (C) Z genes, r = 0.79, A genes, r = 0.29.

Figure 6.

Categorizing chicken Z gene M:F ratios by their degree of difference from zebra finch. (A) Genes were categorized into group 1 with M:F ratios greater in chicken than zebra finch (C>Z, blue), group 2 with M:F ratios similar in the two species (green, >85% of genes), and group 3 with M:F ratios lower in chicken than in zebra finch (C<Z, red). Genes higher in one species were those for which the log₂ M:F ratio was ≥0.25 more in that species than the other. (B) Graph of the three classes of genes by gene order along the Z chromosome of chicken. The region 20–40 Mb was abundant in red spots (C<Z) but lacking in blue spots (C>Z). (C) The proportion of the three classes of genes in four major divisions of the chicken Z chromosomes. Along most of the chromosome regions, red genes (C<Z) were less abundant than blue genes (C>Z), except for the region 20–40 Mb. When gene order was randomized 1000 times, the large difference in proportion of red and blue genes in this interval was found to occur rarely by chance (P < 0.05), whereas the difference in other chromosome regions was not unlikely. The patterns shown here are common to all 12 chicken versus zebra finch comparisons for the three chicken tissues of Itoh et al. (2007) and the four zebra finch telencephalic samples measured here. (D) The ratio of the number of blue (C>Z) to red (C<Z) genes is plotted as a moving average across a window 20 Mb wide (step size 1 Mb) graphed by window center along the Z chromosome. The curve minimum is at 31–32 Mb, near the MHM locus. Thus, the MHM region is unusual because its genes tend to have lower M:F ratios in chicken than zebra finch.