Block party on the zebrafish sex chromosome

John Postlethwait is fascinated by how zebrafish offspring depend on their mom’s genome to get things started. In a study published in the May issue of G3: Genes|Genomes|Genetics, Postlethwait and co-author Catherine Wilson delve into the unique features of the zebrafish sex chromosome, identifying a maternal-to-zygotic-transition (MZT) gene regulatory block.

Zebrafish females are either ZW or WW. ZZ zebrafish are always males, but some fish with a W can sex-reverse to become males. Although sex-biased gene selection is important for understanding characteristics such as sexual dimorphism, little is known about the distribution of sex-biased genes along fish chromosomes.

To learn more about zebrafish sex-biased genes, Wilson and Postlethwait harvested gonads from male and female Nadia-strain zebrafish at three months post-fertilization and performed RNA-seq to compare gene expression patterns in females versus males. Differentially expressed (DE) genes were evaluated with DESeq2 software.

They also analyzed gonads from laboratory strain AB. After several generations of gynogenesis, these fish lack sex chromosomes. Analyzing gonads from AB fish allowed the authors to rule out sex determination as a means of ovary-specific gene silencing.

As expected, substantially more genes showed testis-biased than ovary-biased expression (10,495 to 6,557, respectively). DE genes aligned with these proportions across the genome—with the exception of Chr4, the sex chromosome. Chr4’s long right arm, Chr4R, was cytogenetically and transcriptionally unique. In fact, about 80% of Chr4R genes have no human orthologs.

Importantly, their analysis revealed that a long block of sex chromosome Chr4 features not only the unique silencing of protein-coding genes in egg cells but also encodes RNA molecules for maternal-to-zygotic transfer necessary for making proteins and eliminating the mother’s transcripts.

All egg-laying animals—including, to some extent, humans—begin development using maternally-produced RNA and proteins, which means some embryonic phenotypes depend on the mother’s genotype rather than the embryo’s. The MZT marks the point when the embryo begins to rely on its own RNA and proteins, and it requires complex gene regulation changes.

In contrast to much of the rest of the genome, Chr4R is mainly heterochromatic. Surprisingly, transcription in ovaries was suppressed for nearly all protein-coding genes in this region but still occurred in testes.

This area of suppressed ovary-biased transcription is involved in the MZT transfer of components such as ribosomes and spliceosomes that kickstart embryonic development following fertilization. An adjacent genomic area removes maternal transcripts when the zygote reaches the 1,000-cell stage. 

The study found that gonads from the AB strain followed the same general expression pattern as those from Nadia fish, meaning ovary-specific gene silencing must be related to gonad development, function, or both—not sex determination.

Postlethwait explains that this study lays some groundwork for egg quality research. Pollutants may affect egg quality, and studying non-placental zebrafish makes toxicological effects easier to uncover. Extrapolating such effects to humans requires understanding, among other things, the balance and mechanisms of ovary- and testis-biased expression in developing and adult zebrafish.