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.

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.

rRNAs are non-coding RNAs present in all prokaryotes and eukaryotes. In eukaryotes there are four rRNAs: 18S, 5.8S, 28S, originating from a common precursor (45S), and 5S. We have recently discovered the existence of two distinct developmental types of rRNA: a maternal-type, present in eggs and a somatic-type, expressed in adult tissues. Lately, next-generation sequencing has allowed the discovery of new small-RNAs deriving from longer non-coding RNAs, including small-RNAs from rRNAs (srRNAs). Here, we systemically investigated srRNAs of maternal- or somatic-type 18S, 5.8S, 28S, with small-RNAseq from many zebrafish developmental stages. We identified new srRNAs for each rRNA. For 5.8S, we found srRNA consisting of the 5' or 3' halves, with only the latter having different sequence for the maternal- and somatic-types. For 18S, we discovered 21 nt srRNA from the 5' end of the 18S rRNA with a striking resemblance to microRNAs; as it is likely processed from a stem-loop precursor and present in human and mouse Argonaute-complexed small-RNA. For 28S, an abundant 80 nt srRNA from the 3' end of the 28S rRNA was found. The expression levels during embryogenesis of these srRNA indicate they are not generated from rRNA degradation and might have a role in the zebrafish development.

Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and non-expressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature.

BackgroundRecently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage. On average one embryo per minute was analysed. The focus was on identification and description of the transcriptome dynamics of the expressed genes in this embryonic stage, rather than to biologically interpret profiles in cellular processes and pathways.ResultsIn the late blastula to mid-gastrula stage, we found 6,734 genes being expressed with low variability and rather gradual changes. Ten types of dynamic behaviour were defined, such as genes with continuously increasing or decreasing expression, and all expressed genes were grouped into these types. Also, the exact expression starting and stopping points of several hundred genes during this developmental period could be pinpointed. Although the resolution of the experiment was so high, that we were able to clearly identify four known oscillating genes, no genes were observed with a peaking expression. Additionally, several genes showed expression at two or three distinct levels that strongly related to the spawn an embryo originated from.ConclusionOur unique experimental set-up of whole-transcriptome analysis of 180 individual embryos, provided an unparalleled in-depth insight into the dynamics of early zebrafish embryogenesis. The existence of a tightly regulated embryonic transcriptome program, even between individuals from different spawns is shown. We have made the expression profile of all genes available for domain experts. The fact that we were able to separate the different spawns by their gene-expression variance over all expressed genes, underlines the importance of spawn specificity, as well as the unexpectedly tight gene-expression regulation in early zebrafish embryogenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3672-z) contains supplementary material, which is available to authorized users.

Alternative snRNAs in early zebrafish embryogenesissnRNA, spliceosome, dual translation machinery, embryogenesis 2 1 ABSTRACT 2 Splicing removes intronic RNA sequences are removed from pre-mRNA molecules and 3 enables, by alternative splicing, the generation of multiple unique RNA molecules from a 4 single gene. As such, splicing is an essential part of the whole translation system of a cell. 5 The spliceosome is a ribonucleoprotein complex in which five small nuclear RNAs (snRNAs) 6 are involved; U1, U2, U4, U5, and U6. For each of these snRNAs there are variant gene 7 copies present in a genome. Furthermore, in many eukaryotic species there is an 8 alternative, minor spliceosome that can splice a small number of specific introns. As we 9 previously discovered an embryogenesis-specific ribosomal system in zebrafish early 10 embryogenesis based on variant rRNA and snoRNA expression, we hypothesized that there 11 may also be an embryogenesis-specific spliceosome. An inventory of zebrafish snRNA genes 12 revealed clustered and dispersed loci for all but U2 major snRNAs. For each minor 13 spliceosome snRNA, just one gene locus was found. Since complete snRNA molecules are 14 hard to sequence, we employed a combined PCR-sequencing approach to measure the 15 individual snRNA-variant presence. Analysis of egg and male-adult samples revealed 16 embryogenesis-specific and somatic-specific variants for each major snRNA. These variants 17 have substantial sequence differences, yet none in their mRNA binding sites. Given that 18 many of the sequence differences are found in loop structures indicate possible alternative 19 protein binding. Altogether, with this study we established that the spliceosome is also an 20 element of the embryogenesis-specific translation system in zebrafish. 21 22 23 24 25 26 27 3 28 INTRODUCTION29 Alternative splicing is fundamental for gene regulation and the generation of different 30 transcripts and/or proteins from an individual gene in eukaryotes (1). Splicing is executed by 31 the spliceosome and removes intronic sequences from pre-mRNA during the maturation 32 process in which the exonic sequences eventually form the mRNA (2,3).The spliceosome is a 33 molecular complex formed by hundreds of proteins and five essential small-nuclear RNAs 34 (snRNAs) that are typically located in the nucleus. The size of these small RNA molecules 35 ranges from 118 nucleotides (nt) to 191 nt. As they are uracil rich, they are called U1, U2, 36 U4, U5 and U6 snRNAs. Next to this major spliceosome, a minor (or U12 dependent) 37 spliceosome exists in many eukaryotic species, which is involved in the splicing of a relative 38 small number of specific introns (4). The snRNAs involved in the minor spliceosome are: 39 U11, U12, U4atac, and U6atac, completed by the U5 from the major spliceosome (4).40 As splicing is at the core of the cellular translation system, the sequences of the involved 41 snRNA are highly conserved across species. At the same time, many non-canonical variants 42 and gene copies of the major s...

Maternal-and somatic-type snoRNAs in zebrafishU3 U8 snoRNA, maternal expression, RNA processing, embryogenesis 1 ABSTRACT 2 Small nucleolar RNAs (snoRNAs) are non-coding RNAs that play an important role in the 3 complex maturation process of ribosomal RNAs (rRNAs). SnoRNAs are categorized in classes, 4 with each class member having several variants present in a genome. Similar to our finding 5 of specific rRNA expression types in zebrafish embryogenesis, we discovered preferential 6 maternal-and somatic-expression for snoRNAs. Most snoRNAs and their variants have 7 higher expression levels in somatic tissues than in eggs, yet we identified three snoRNAs; 8 U3, U8 and snoZ30 of which specific variants show maternal-or somatic-type expression.9 For U3 and U8 we also found small-derived snoRNAs that lack their 5' rRNA recognition part 10 and are essentially Domain II hairpin structures (U-DII). These U-DII snoRNAs from variants 11 showed similar preferential expression, in which maternal-type variants are prominently 12 expressed in eggs and subsequently replaced by a somatic-type variants during 13 embryogenesis. This differential expression is related to the organization in tandem repeats 14 (maternal type) or solitary (somatic-type) genes of the involved U snoRNA loci. The 15 collective data showed convincingly that the preferential expression of snoRNAs is achieved 16 by transcription regulation, as well as through RNA processing. Finally, we observed small-17 RNAs derived from internal transcribed spacers (ITSs) of a U3 snoRNA loci that via 18 complementarity binding, may be involved in the biosynthesis of U3-DII snoRNAs.19 Altogether, the here described maternal-and somatic-type snoRNAs are the latest addition 20 to the developing story about the dual ribosome system in zebrafish development. 22 INTRODUCTION23 Small nucleolar RNAs (snoRNAs) are a class of non-coding RNA molecules of variable length 24 (the majority being 60-200 nucleotides long), found in archaea and eukaryotes (1). SnoRNAs 3 25 are thought to mainly be involved in post-transcriptional modifications and maturation of 26 ribosomal RNAs (rRNAs) (2,3). However, recently additional functions have been ascribed to 27 specific snoRNAs, from regulation of mRNA editing and splicing (4) to post-transcriptional 28 gene silencing (5,6). SnoRNAs do not possess any intrinsic catalytic or modification activity, 29 but act both as a scaffold for partner proteins, forming small nucleolar ribonucleoproteins 30 (snoRNPs) and as guide for target specificity (7). Based on base-pairing interactions with 31 their target RNA, snoRNAs can thus direct the associated catalytic protein subunits to 32 accurately modify a specific RNA site (8).33 In general, eukaryotic genomes can contain up to 200+ unique snoRNA genes (9). Based on 34 the presence of conserved sequence motifs, the majority of snoRNAs are classified into two 35 distinct classes: box C/D snoRNAs, which guide 2'-O-methylation of ribose, and box H/ACA 36 snoRNAs, which are involved in the isomerization of sp...

Cellular translation relies heavily on the involvements of several types of non-coding RNAs.In previous studies we have identified a dual translation system in zebrafish development, involving maternal-type and somatic-type rRNAs, snoRNAs, and snRNAs. In this study we focused on several remaining non-coding RNAs involved in the translation system; tRNAs, RNase P, and SRP RNA. Even though our studies have been limited in extent, for all three types of non-coding RNA we were able to identify a maternal-specific type, with substantial sequence differences as compared to the somatic-type variant. Hence, these RNA types complement the previously discovered RNA types in the unique dual translation system in zebrafish development.