Advancements in pseudouridine modifying enzyme and cancer

Abstract

Pseudouridine (Ψ) is a post-transcriptional modifier of RNA, often referred to as the 'fifth nucleotide' owing to its regulatory role in various biological functions as well as because of its significant involvement in the pathogenesis of human cancer. In recent years, research has revealed various Ψ modifications in different RNA types, including messenger RNA, transfer RNA, ribosomal RNA, small nuclear RNA, and long noncoding RNA. Pseudouridylation can significantly alter RNA structure and thermodynamic stability, as the Ψ-adenine (A) base pair is more stable than the typical uridine (U)-A base pair is due to its structural similarity to adenine. Studies have linked Ψ expression to the development and progression of several digestive system cancers, such as liver cancer and colorectal cancer, and nondigestive system cancers, such as breast cancer, non-small cell lung cancer, prostate cancer, glioblastoma, ovarian cancer, oral squamous cell carcinoma, and pituitary cancer. The present review briefly outlines the chemical structure, synthesis, and regulatory mechanisms of Ψ. This review summarizes the effects of pseudouridylation on various substrates of RNA and briefly discusses methods for detecting Ψ. Last, it focuses on how RNA pseudouridylation influences different cancers, emphasizing the search for novel approaches to cancer diagnosis, treatment, and prognosis through Ψ modification.

Keywords: RNA; epigenetics; pseudouridine; pseudouridine-modifying enzyme; tumor.

FIGURE 1

Mapping of RNA modifications and RNA pseudouridylation machinery. (A) There are many ways that RNA can be modified, such as N6-methyladenine (m6A), N1-methyladenine (m1A), 5-hydroxymethylcytosine (hm5C), Ψ, etc. (B) Schematic depiction of RNA pseudouridylation reaction catalyzed by PUS. PUS mediate the isomerization of U to ψ, which results in an extra hydrogen bond donor (B) and the same number of hydrogen bond acceptors (A). (C) Water-mediated hydrogen-bond network. Schematic depiction of the Ψ-specific, water-mediated hydrogen-bond network. The water molecule and positions of the base and the sugar are indicated. (D) The mechanism of Ψ regulation. There are two main ways of pseudouracilylation of RNA substrates in eukaryotes.

FIGURE 2

The role of pseudouracil in mRNA metabolism. Mechanism diagram of a Radiolabeling-Free, qPCR-Based Method for Locus-Specific Pseudouridine Detection. (A) Pseudouridine (Ψ) impacts multiple facets of mRNA metabolism such as pre-mRNA splicing, RNA stability, and translation. Ψ can affect the local mRNA structure of sub-strate RNA and thereby regulate its mRNA stability. Very often, pseudouridylated mRNA codons are associated with unusual base pairing, which alters the fidelity of translation. Further, pre-mRNA pseudouridylation can affect the splicing machinery and thus regulate alternative splicing. (B) Workflow of the method (qPCR-Based). Y-containing RNA is specifically labeled by CMC, and then reverse transcribedbySuperscriptII(SSII) with Mn2+ buffer.The Y–CMC adducts cause SSII to introduce amutation/deletion at or around the Y site in the synthesized cDNA, thus giving rise to anew peak (indicated by the red arrow) in the melting curve of qPCR products.

FIGURE 3

The mechanism of pseudouracil modification enzyme and cancer. (A) Diagram summarizing cancers covered in the review and their associated pseudouridine regulatory factor. (B) The regulatory mechanism of pseudouridine in Hepatic cancer. (C) The regulatory mechanism of pseudouridine in Colorectal cancer. (D) The regulatory mechanism of pseudouridine in Glioblastoma.