Abstract
The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will present a nonexhaustive list of referenced small non-coding RNAs (ncRNAs) derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs). We will focus on the rRFs that are experimentally verified, and discuss their origin, length, structure, biogenesis, association with known regulatory proteins, and potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because no one could believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.
Highlights
The ribosomes are ribonucleoprotein (RNP) complex assemblies required for the translation of all proteins [1,2]
In humans, there are approximately 300–400 ribosomal DNA (rDNA) repeats in five clusters on chromosomes 13, 14, 15, 21, and 22 [8], potentially explaining the ribosomal RNA (rRNA) sequence variability. This variability has notably been reported by Wang et al [10], who calculated the coefficient of variation (CV) of the average depth among samples in the 18S and 28S rRNA, which they reported as a diagram of variability as a function of the sequence region [10]
The importance of non-coding RNAs (ncRNAs) in cellular regulatory mechanisms, especially during ribosome biogenesis, and their contribution to ribosome heterogeneity, both compositional and functional [21], raised a particular interest in this field of study. These studies range from the small RNAs like the small nucleolar RNAs (snoRNAs) [19] (HBII-95, HBII-234, etc.), which contribute to the rRNA maturation, notably by inducing biochemical changes on the rRNA sequence, to the large RNAs like the nucleolar-specific lncRNA (LoNA), which can suppress rRNA transcription and reduce rRNA methylation [54]
Summary
The ribosomes are ribonucleoprotein (RNP) complex assemblies required for the translation of all proteins [1,2]. Ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function [3]. This surface may be an interface for interacting proteins, as suggested by the identification of hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes [4]. RRNA sequences may be modified, as the presence of ufmylation suggests [4], or be cleaved to form new functional small non-coding RNAs (ncRNAs) species. The interplay between RAPs, biochemical changes, and generation of new small ncRNAs may provide an additional layer of regulation and govern one of life’s most ancient molecular machines involved in protein expression [5,6]
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