Distinct maternal and somatic rRNA types in zebrafish development

There is mounting evidence that the ribosome is not a static translation machinery, but a cell-specific, adaptive system. Ribosomal variations have mostly been studied at the protein level, even though the essential transcriptional functions are primarily performed by ribosomal RNAs (rRNAs). At the RNA level, oocyte-specific 5S rRNAs are long known for Xenopus. In this thesis, through a next-generation sequencing study on zebrafish egg, embryo and adult tissue, we initially identify maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. Moreover, for the first time, we report the discovery of an analogous system for the 45S rDNA elements; 5.8S, 18S, and 28S. The maternal-type rRNAs differ substantially from those of the somatic-type not only by several nucleotides but also by their chromosome location and genomic organization. We discuss the structural and functional implications of the observed sequence differences with respect to the translational functions of all the rRNA elements. Additionally, we describe several small RNAs derived from the maternal- and somatic-type rRNAs (srRNAs) and characterize their expression during the zebrafish development. The features of these srRNAs indicate that they are not generated from rRNA degradation and thus might have a functional role.
Taken together, our findings indicate that two distinct types of ribosomes exist in zebrafish during development, each likely conducting the translation machinery in a unique way.