Dosage Compensation throughout the Schistosoma mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome

Abstract

Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3, and H4K20me1 histone marks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.

Keywords: Schistosoma mansoni; chromatin landscape; dosage compensation; female heterogamety; histone modifications.

Fig. 1.

—Gene expression level according to sex, developmental stage, and genomic location. Three developmental stages of the parasite are shown (A): cercariae are free larvae without any sexual dimorphism (1); schistosomula represent an intravertebrate stage, with ongoing sexual differentiation but no phenotypic sexual dimorphism (2); and immature worms are sexually differentiated but sexually non-functional as they did not mate (3). Expression of autosomal genes (“A,” dark shade), pseudoautosomal genes (“PAR,” dark shade), and Z-specific genes (“Z,” light shade) is represented considering female-to-male ratio (“F:M”) (B), or independently within females (C) and males (D). Only genes with expression RPKM > 1, and a female-to-male fold change lower than 2 (sex-bias filtering) are taken into account (n = 3,741 in cercariae; n = 5,636 in schistosomula; n = 5,657 in immature worms). The Z-to-autosome expression ratio for each sex (Z:AA for female, and ZZ:AA for male), and the corresponding female-to-male ratio (Z[F:M]/A[F:M]) are detailed in table 2 (“RPKM > 1 - sex-bias filtered”). Asterisks show the level of significance for each of these comparisons (Wilcoxon test): *P value < 0.05, **P value < 0.001, and ***P value < 0.0001.

Fig. 2.

—Gene expression pattern according to the location along the Z chromosome, and the developmental stages. The female-to-male expression ratio (F:M) is represented for the three Z-specific regions defined in the version 5.2 of the genome (Z1 in light beige, Z2 in orange, and Z3 in light beige) and the PAR (in dark beige) for cercariae (A), schistosomula (C), and immature worms (E). For each stage, gene expression pattern for female (in pink) and male (in blue) is shown along the Z by sliding window of 50 genes (B, D, F). The thick black line represents the female-to-male expression ratio by sliding window of 50 genes. Only genes with expression RPKM > 1 and a sex-bias fold change <2 are shown. Asterisks show the level of significance of Z-to-PAR comparisons (Wilcoxon rank sum test with continuity correction): ***P value < 0.0001, N.S. = nonsignificant differences. Z1-to-PAR ratio values are 0.76, 0.72, and 0.64; Z2-to-PAR ratio values are 0.88, 0.71, and 0.62; Z3-to-PAR ratio values are 0.81, 0.74, and 0.62, for cercariae, schistosomula, and immature worms, respectively. Other ratios are shown in Supplementary Table 2, Supplementary Material online.

Fig. 3.

—Average H3K4me3 and H3K27me3 enrichment profile according to sex, developmental stage, and genomic location. x axis represents the position in base pairs (bp) relative to the TSS of the genes (position 0). y axis represents the normalized average enrichment of reads obtained after a Chromatin Immunoprecipitation targeting the “permissive” mark H3K4me3 (in green) and the “nonpermissive” H3K27me3 (in red), in female cercariae (A) and immature worms (B), or male cercariae (C) and immature worms (D). The EpiChIP enrichment has been calculated around the TSS for chromosome 1 as proxy for autosomes (Chr1, dark shade), for the PAR of sex chromosomes (PAR, medium shade), and for chromosome Z-specific region of sex chromosomes (Z, light shade). For each of these genomic locations, we show the average result of the profiles obtained for each coding sequence. Each profile has been normalized with the same average enrichment of reads obtained after a Chromatin Immunoprecipitation without antibody. The experiment was performed in duplicates in males and triplicate in females. EpiChIP profiles showing standard error at each position are shown in Supplementary Figures 6 and 7, Supplementary Material online. The percentage of maximum difference between genomic regions is shown in Supplementary Tables 3 and 4, Supplementary Material online: all differences are statistically significant (P value < 0.001, Kolmogorov–Smirnov two sample tests).