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

• Published in: Genome Vol. 61; no. 5; pp. 371 - 378
• Main Authors: Locati, Mauro D, Pagano, Johanna F.B, Abdullah, Farah, Ensink, Wim A, van Olst, Marina, van Leeuwen, Selina, Nehrdich, Ulrike, Spaink, Herman P, Rauwerda, Han, Jonker, Martijs J, Dekker, Rob J, Breit, Timo M
• Format: Journal Article
• Language: English
• Published: Canada NRC Research Press 01.05.2018; Canadian Science Publishing NRC Research Press
• Subjects: adults; Animals; Argonaute Proteins - genetics; Argonaute Proteins - metabolism; ARN ribosomique; Base Sequence; Danio rerio; development; Developmental stages; dérivés de petits ARNr; développement; Eggs; Embryo, Nonmammalian - metabolism; Embryogenesis; embryogenèse; Embryonic Development - genetics; Embryonic growth stage; Eukaryotes; eukaryotic cells; Expressed sequence tags; Fish; Gene Expression Regulation, Developmental; Genes; Genetic aspects; Genomes; High-Throughput Nucleotide Sequencing; humans; Methods; mice; microRNA; miRNA; Next-generation sequencing; non-coding RNA; Nucleic Acid Conformation; Physiological aspects; poisson-zèbre; Precursors; Prokaryotes; prokaryotic cells; Protein Binding; Ribonucleic acid; Ribosomal RNA; RNA; RNA sequencing; RNA, Ribosomal, 18S - genetics; RNA, Ribosomal, 18S - metabolism; RNA, Ribosomal, 28S - genetics; RNA, Ribosomal, 28S - metabolism; RNA, Ribosomal, 5.8S - genetics; RNA, Ribosomal, 5.8S - metabolism; RNA, Small Untranslated - genetics; RNA, Small Untranslated - metabolism; rRNA 18S; rRNA 28S; rRNA 5.8S; small-rRNA derived; Studies; tissues; Zebrafish; Zebrafish - genetics; Zebrafish - growth & development; Zebrafish - metabolism; Zygote - growth & development; Zygote - metabolism; development; développement; embryogenesis; ribosomal RNA; ARN ribosomique; small-rRNA derived; zebrafish; dérivés de petits ARNr; poisson-zèbre; embryogenèse
• ISSN: 0831-2796; 1480-3321; 1480-3321
• DOI: 10.1139/gen-2017-0202

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.