Regulation and Function of RNA Pseudouridylation in Human Cells

Abstract

Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.

Keywords: RNA modification; innate immunity; mRNA; pseudouridine; snRNA; tRNA; translation.

Figure 1.. Chemical structures of uridine and pseudouridine

Figure 2.. tRNA pseudouridylation.

Biochemically identified Ψ sites in cytoplasmic (A) and mitochondrial (B) human tRNAs are marked by shaded circles with the PUS indicated where known. Sites identified exclusively by high-throughput sequencing are shown as open circles.

Figure 3.. Pseudouridine is catalyzed by human PUS.

Domain schematic of human PUS grouped and color coded by family.

Figure 4.. RPUSD3 lacks a catalytic aspartate:

(A) Multiple sequence alignment of human RluA family members and E. coli RluA. The HRLD motif is denoted by a line above the alignment and the position of the catalytic aspartate is indicated by the asterisk (*). (B-G) An overlay (B) or individual structures of the catalytic pocket of E. coli RluA (B, PDB 2I82), human RPUSD3 (C, model), RPUSD1 (E, PDB 5VBB), RPUSD2 (F, model), and RPUSD4 (G, PDB 5UBA). The residues at the catalytic and salt bridge positions are shown as sticks. The structure of E. coli RluA includes 5FU in position of the pseudouridylated residue. Models were generated using SwissModel. The multiple sequence alignment was generated using ClustalOmega and formatted using BoxShade.

Figure 5.. Expression of human PUS across human tissues.

Gene expression in transcripts per million (TPM) of the 13 human pseudouridine synthases across different tissue types. PUS are clustered based on expression similarity. The figure was created using the GTEx Portal on 02/13/2020