New observations on non-coding RNAs involved in the dual translation system in zebrafish development

Abstract

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.

tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development

“…Similarly, C34 in mt-Met-CAT is expected to be methylated to m 5 C by NSUN3 and then further modified to f 5 C, although the extent of formylation in human cells was subject to dispute (reviewed in (47)). We clearly detected C retention at C34 of mt-Met-CAT (Figure 6), again suggesting that either the site is only partially formylated, or it is further reduced to hm 5 C. Finally, we detected signature of m 5 C methylation at C72 of Cys-GCA and all Thr clusters (Figure 6), which are known targets of NSUN6 (48), and at C38 of Asp-20 GTC and Gly-GCC/CCC, and to a lower extent of Val-AAC/TAC, which are expected to be methylated by DNMT2 (49)(50)(51).…”

“…Noteworthy, the expression of ribosomal RNAs has been shown to be heavily regulated during development in vertebrates, with distinct sets of rRNA genes being expressed in the oocyte and early stages of embryonic development versus later embryonic stages and adult zebrafish (3,4). While similar findings were recently reported also for other non-coding RNAs (5)(6)(7), reliable data on tRNAs remain scarce and under-represented in transcriptomic studies.…”

“…The methylation m 5 C was shown to be important for RNA folding and metabolism, and alterations in the expression/function of m 5 C-installing methyltransferases was linked to developmental defects and cancer (reviewed in (39) and ( 10)), attracting broad interest. However, previous studies on m 5 C methylation in embryo development have focused on mRNAs (40,41), and the elucidation of the tRNA m 5 C methylome, in particular in vertebrate embryo development, remained unexplored.…”

“…NSUN2 also methylates C34 of nucleo-cytoplasmic tRNA-Leu-CAA, which is then further modified to 2′-0-methyl-5formylcytidine (f 5 Cm) (44). After bisulfite treatment, f 5 Cm is not expected to be detected as C retention in NGS data like m 5 C, unless an additional protection or reduction step is included in the protocol (45). In the BS libraries, we detected modification signature in the form of C retention at C34 of the cluster Leu-CAA (Figure 6, Supplementary File 4), suggesting that in zebrafish this site is either only partially formylated, or is further reduced to 5-hydroxymethylcytosine (hm 5 C), which behaves like m 5 C in bisulfite treatment and sequencing (46).…”

Immunoglobulin switch-like recombination regions implicated in the formation of extrachromosomal circular 45S rDNA involved in the maternal-specific translation system of zebrafish

“…Over the last years, we have reported on the discovery of an intriguing dual translation system in zebrafish development (Locati et al 2017a(Locati et al , 2017b(Locati et al and 2018Pagano et al 2019a and2019b;Breit et al 2019). The two systems encompass at least all essential non-coding RNA containing components of the translation process: the spliceosomes (snRNA) (Pagano et al 2019b); the ribosomes (5S, 5.8S, 18S, and 28S rRNA) (Locati et al 2017a(Locati et al , 2017b(Locati et al and 2018 plus the pre-rRNA processing snoRNAs (Pagano et al 2019a); the tRNAs (Breit et al 2019) plus the pre-tRNA processing RNaseP (Breit et al 2019); and the Signal Recognition Particle (SRP-RNA) for translocation of the translational complex to the ER (Breit et al 2019). Of this dual translation system, the maternal-type variant (45S-M) is produced during oogenesis and progressively replaced by the somatic-type variant (45S-S) during embryogenesis (Locati et al 2017b, Ortega-Recalde et al 2019.…”