A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome

Abstract

Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex determination system with the major sex locus on the right arm of chromosome-4 (Chr4R) near the largest heterochromatic block in the genome, suggesting the hypothesis that the Chr4R transcriptome might be different from the rest of the genome. We conducted an RNA-seq analysis of adult ZW ovaries and ZZ testes and identified four regions of Chr4 with different gene expression profiles. Unique in the genome, protein-coding genes in a 41.7 Mb section (Region-2) were expressed in testis but silent in ovary. The AB lab strain, which lacks sex chromosomes, verified this result, showing that testis-biased gene expression in Region-2 depends on gonad biology, not on sex-determining mechanism. RNA-seq analyses in female and male brain and liver validated few transcripts from Region-2 in somatic cells, but without sex-specificity. Region-2 corresponds to the heterochromatic portion of Chr4R and its content of genes and repetitive elements distinguishes it from the rest of the genome. In Region-2, protein-coding genes lack human orthologs; it has zinc finger genes expressed early in zygotic genome activation; it has maternal 5S rRNA genes, maternal spliceosome genes, a concentration of tRNA genes, and an distinct set of repetitive elements. The colocalization of 1) genes silenced in ovaries but not in testes that are 2) expressed in embryos briefly at the onset of zygotic genome activation; 3) maternal-specific genes for translation machinery; 4) maternal-specific spliceosome components; and 4) adjacent genes encoding miR-430, which mediates maternal transcript degradation, suggest that this is a Maternal-to-Zygotic-Transition Gene Regulatory Block.ARTICLE SUMMARYThe wild zebrafish sex chromosome has a region, unique in the genome, that contains protein-coding genes silenced in ovaries but expressed in testes and transiently in the embryo as it begins to express its own genes. This region also contains maternal-specific genes encoding the protein-synthesis machinery used specifically by developing embryos, and molecules that target for degradation messenger RNAs that the mother stored in her eggs. This region defines a distinct maternal-to-zygotic-transition gene block.

Direct male development in chromosomally ZZ zebrafish

“…Unlike laboratory strains, zebrafish lines not long adapted to laboratory life at the time of investigation, including the Nadia (NA) strain, have a genetic ZZ/ZW sex determination system, with the major Sex-Associated Region on chromosome-4 ( sar4 ) located near the telomere of the right arm of chromosome-4 (Chr4) (as displayed in Ensembl: (ensembl.org/Danio_rerio/Location/Chromosome?r=4) ( Tong et al, 2010 ; Anderson et al, 2012 ; Wilson et al, 2014 ), a chromosome that has, in addition to the sex locus, a region that has sex-specific silencing of protein-coding gene transcription in ovaries ( Wilson and Postlethwait, 2023 ). Individual NA strain zebrafish homozygous for Z alleles always develop as males and most ZW individuals become females, but some ZW individuals develop as males in all four strains investigated ( Anderson et al, 2012 ; Wilson et al, 2014 ).…”