Persistence of oocyte amplified rDNA during early development of Xenopus laevis eggs

Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during 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 rRNAs. At the RNA level, oocyte-specific 5S rRNAs are long known for Xenopus. Recently, we described for zebrafish a similar system in which the sole maternal-type 5S rRNA present in eggs is replaced completely during embryonic development by a somatic-type. Here, we report the discovery of an analogous system for the 45S rDNA elements: 5.8S, 18S, and 28S. The maternal-type 5.8S, 18S, and 28S rRNA sequences differ substantially from those of the somatic-type, plus the maternal-type rRNAs are also replaced by the somatic-type rRNAs during embryogenesis. We discuss the structural and functional implications of the observed sequence differences with respect to the translational functions of the 5.8S, 18S, and 28S rRNA elements. Finally, in silico evidence suggests that expansion segments (ES) in 18S rRNA, previously implicated in ribosome-mRNA interaction, may have a preference for interacting with specific mRNA genes. 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.

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified 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. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci.

Patterns of transcriptional activity of nucleolar genes during progesterone-induced maturation of oocytes of Xenopus laevis

Maturation has been induced in full grown oocytes of Xenopus laevis by incubation in progesterone, and the ultrastructure of their nucleoli has been examined by electron microscopy using the chromatin spreading technique. We show that in this species numerous extrachromosomal nucleoli maintain high levels of transcription of rDNA for up to 200 min after the application of the hormone, i.e., shortly before germinal vesicle breakdown. Transcription has been identified as normal arrays of matrix units containing densely packed transcriptional complexes. In addition to normal-sized arrays of gradients of nascent RNP fibrils, as typical of active pre-rRNA genes, a number of unusual structures are described which include situations of sparse coverage of lateral fibrils in some matrix units, indicative of reduced frequencies of initiation events. The observations are discussed in relation to the time course of nucleolar gene inactivation described in oocytes of other amphibian species, as well as in relation to inactivation of chromosomal genes characteristic of this step of meiotic prophase I.