Identifying small RNAs derived from maternal- and somatic-type rRNAs in zebrafish development

Abstract

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.

An alternative spliceosome defined by distinct snRNAs in early zebrafish embryogenesis

“…In earlier studies we discovered cellular components related to the transcription machinery that have distinct embryogenesis expression or somatic expression during zebrafish development. We reported on 5S (26), 5.8S, 18S, and 28S (27), plus small-derived components from those molecules (28), as well as snoRNAs (25). As it is clear that in zebrafish oogenesis and early embryogenesis a different transcription machinery is employed, it is obvious to investigate other components of this system.…”

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

“…In this manuscript, we presented the preliminary results of our initial gene-expression analyses of the non-coding RNA types involved in the zebrafish translation system, other than we previously reported on (Locati et al 2017a(Locati et al , 2017b(Locati et al , 2018Pagano et al 2019bPagano et al , 2019a. Alike rRNA (Locati et al 2017a(Locati et al , 2017b, snoRNA (Pagano et al 2019b), and snRNA (Pagano et al 2019a), the investigated tRNA, RNase-P and SRP-RNA all seem to have a maternal-specific variant.…”

“…This maternaltype 5S RNA variant is gradually replaced throughout embryonic development by a somatictype variant (Wegnez et al 1972;Brown et al 1977;Wormington and Brown 1983;Guinta et al 1986;Komiya et al 1986). Starting from this long-standing observation, our continuous studies reported in several manuscripts (Locati et al 2017a(Locati et al , 2017b(Locati et al , 2018Pagano et al 2019bPagano et al , 2019a show the existence of a specialized maternal-type translation system in zebrafish far beyond just 5S rRNA. One by one, we have revealed that also the translation-involved non-coding RNAs 5.8S, 18S, 28S, snoRNA, and snRNA are implicated in this maternal-type translation system ( Figure 1 and Table 1).…”

MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis

“…Notably, miRNA-like molecules interchangeably called small rDNA-derived RNAs or rRNA-hosted miRNA analogs (srRNAs or rmiRNAs) derive from precursor and mature rRNAs through poorly understood mechanisms ( Figure 2C) [5,6]. srRNA/rmiRNA generation is likely not due to random degradation but rather controlled processing that creates stable srRNA products, and may be Drosha-dependent or independent [6][7][8]. Functionally, rmiRNAs have been shown to bind AGO proteins and are implicated in the regulation of various metabolic and developmental pathways.…”