UC Berkeley

Many species determine sex by assessing sex-chromosome dose. In flies, mammals, and nematodes, males have one X chromosome and females or hermaphrodites have two. However, both sexes require the same level of expression for most genes; thus they evolved a process called dosage compensation to equalize X-linked gene expression between the sexes. Failure to carry out this process causes lethality in one sex. Flies, mammals, and nematodes have independently evolved very different dosage compensation mechanisms, showing that multiple strategies can be employed to achieve dosage compensation. We chose to investigate four nematode species with shared ancestry to ask whether and how essential dosage compensation mechanisms are able to evolve over time. Examples of dosage compensation mechanisms in closely related species provide evidence to better understand how genes with different expression constraints can be regulated simultaneously across chromosome-wide territories.

Here, I compare chromosome-wide dosage compensation mechanisms across four Caenorhabditis species (less than 30 million years diverged): C. elegans}, C. briggsae, C. nigoni, and C. tropicalis. We took advantage of improved sequencing technology to create chromosome-level genome assemblies for C. nigoni and C. tropicalis. We also devised genome editing strategies for the non-model species C. briggsae, C. nigoni, and C. tropicalis. Using genome editing, we created strains for phenotypic and biochemical assays to assess the function of orthologous genes in dosage compensation. Key subunits of the dosage compensation machinery and the genetic hierarchy that regulates the sex-specific function of the machinery share conserved action across species. However, remarkably, the binding sites on the X chromosome and the DNA sequence motifs within binding sites that drive X-specific binding have diverged at least twice within 30 million years of evolution. Since the dosage compensation machinery acts to modify the structure of the C. elegans X chromosome by bringing binding sites together, divergence in binding site location could result in a different X-chromosome structure in these species. Future studies of the rapid divergence of binding sites that characterize X-chromosome structure and X-linked gene expression could bring us closer to understanding how nematode dosage compensation operates.