RNA modifications: a mechanism that modulates gene expression

Abstract

Accuracy in the flow of genetic information from DNA to protein, or gene expression, is essential to the viability of an organisms. Pre-mRNA splicing and protein translation are two major steps in eukaryotic gene expression that necessitate the production of accurate gene products. Both processes occur in large complexes, consisting of both proteins and noncoding RNAs. Interestingly, the RNA components contain a large number of posttranscriptional modifications, including 2'-O-methylation and pseudouridylation, which are functionally important. In this chapter, we highlight the functional aspects of the modifications of spliceosomal snRNA and rRNA and provide a framework for understanding how posttranscriptional modifications are capable of influencing gene expression.

Fig. 1.1

Schematic depiction of the two most abundant modified nucleotides in snRNA and rRNA. (Top) Pseudouridine is a rotational isomer of uridine, in which the C–C glycosidic bond is broken to form an N–C bond, resulting in the presence of an extra hydrogen bond donor (d) while the number of hydrogen bond acceptors (a) is unchanged. (Bottom) Schematic representation of a 2′-O-methylated ribose.

Fig. 1.2

Primary sequences and secondary structures of the vertebrate major spliceosomal snRNAs. Positions of pseudouridine residues are marked in boxes and 2′-O-methylated nucleotides are circled. The 5′ caps (2,2,7-trimethylated guanosine cap for U1, U2, U4, and U6, and a γ-methylated guanosine for U6) are also shown. The pseudouridine residues in U2 and U1 snRNAs that are conserved in yeast are marked with arrows. The thick line indicates the U2 branch site recognition region.

Fig. 1.3

Secondary structure depiction of S. cerevisiae cytoplasmic ribosome (modified from (37)). The 18S rRNA is depicted on the left, while the 25S–5.8S is shown on the right. The PTC, ASF, and Helix 69 are apparent in the structure. Modification sites in the rRNA species are illustrated as follows: pseudouridylation sites (ψ) – gray squares and 2′-O-methylation sites (Nm) – black triangles.

Fig. 1.4

Schematic depiction of box H/ACA and C/D RNAs. (a) Minimal components of a eukaryotic pseudouridylation guide H/ACA. The RNA adapts a Hairpin-Hinge-Hairpin-Tail structure. Present within the hinge region is the box H, the ACA motif typically lies three nucleotides from the 3′-end of the RNA. Pseudouridylation is targeted to substrate RNAs by complementary basepairing interactions between the internal loop (pseudouridylation pocket) and nucleotides flanking the target uridine. (b) Secondary structure of a box C/D RNA. Boxes C, D, C′, and D′ are shown. The 2′-O-ME represents the target 2′-O-methylation site that is always the fifth nucleotide from box D or D′.