The cellular landscape of mid-size noncoding RNA

Abstract

Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.

Keywords: mid-size noncoding RNA; noncoding RNA; snRNA; snoRNA; tRNA.

Figure 1

Types and size distribution of human RNA. The different types of human RNAs are illustrated as a function of their length. The average size of small, mid‐size and long RNA is indicated in red, green and blue boxes, respectively. Dotted lines indicate the size delimitation between these RNA families. The median size of mRNAs and the size of rRNAs that are too large to be visible on the figure are indicated on the right

Figure 2

Schematics of the evolutionary history of human mncRNA. The vertical time‐scale is a descriptive representation (not to scale) of the appearance time of different RNA types with the bottom representing the RNA world and the top representing human‐specific RNA. Eukaryotic branches close to the human lineage are indicated in light green while those further away are indicated in dark green. The branching events relevant to the appearance of the different types of mncRNA are indicated on the right

Figure 3

Summary of the RNA contents in mncRNA databases. The RNA content found in major genome annotation databases is indicated

Figure 4

Key features of major human mncRNA annotation databases. General information for each database, as of December 2018, including methods for data accession, data type and release dates, are indicated