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

Area of Science:

• Molecular Biology
• Developmental Biology
• Genetics

Background:

• Ribosomal RNAs (rRNAs) are essential non-coding RNAs in all cells.
• Eukaryotes possess four main rRNAs (18S, 5.8S, 28S, 5S), with 18S, 5.8S, and 28S originating from a 45S precursor.
• Two developmental rRNA types, maternal and somatic, have been identified.

Purpose of the Study:

• To systematically investigate small RNAs derived from maternal and somatic ribosomal RNAs (srRNAs) in zebrafish.
• To characterize novel srRNAs originating from 18S, 5.8S, and 28S rRNAs across various developmental stages.
• To explore the potential roles of these srRNAs in zebrafish development.

Main Methods:

• Small RNA sequencing (small-RNAseq) was performed on multiple zebrafish developmental stages.
• Bioinformatic analysis was used to identify and characterize srRNAs.
• Expression levels of identified srRNAs were analyzed during embryogenesis.

Main Results:

• Novel srRNAs were identified for 18S, 5.8S, and 28S rRNAs.
• A 5.8S srRNA was found to consist of 5' or 3' halves, with sequence differences in the 3' half between maternal and somatic types.
• A 21-nucleotide srRNA from the 18S rRNA 5' end resembles microRNAs and is found in zebrafish, human, and mouse Argonaute complexes.
• An abundant 80-nucleotide srRNA from the 28S rRNA 3' end was identified.

Conclusions:

• The identified srRNAs are not products of rRNA degradation, as indicated by their expression patterns during embryogenesis.
• These novel srRNAs likely play a functional role in zebrafish development.
• The discovery of microRNA-like srRNAs from 18S rRNA opens new avenues for understanding gene regulation.