The tRNA pseudouridine synthase TruB1 regulates the maturation of let‐7 miRNA

Abstract

Let-7 is an evolutionary conserved microRNA that mediates post-transcriptional gene silencing to regulate a wide range of biological processes, including development, differentiation, and tumor suppression. Let-7 biogenesis is tightly regulated by several RNA-binding proteins, including Lin28A/B, which represses let-7 maturation. To identify new regulators of let-7, we devised a cellbased functional screen of RNA-binding proteins using a let-7 sensor luciferase reporter and identified the tRNA pseudouridine synthase, TruB1. TruB1 enhanced maturation specifically of let-7 family members. Rather than inducing pseudouridylation of the miRNAs, high-throughput sequencing crosslinking immunoprecipitation (HITS-CLIP) and biochemical analyses revealed direct binding between endogenous TruB1 and the stem-loop structure of pri-let-7, which also binds Lin28A/B. TruB1 selectively enhanced the interaction between pri-let-7 and the microprocessor DGCR8, which mediates miRNA maturation. Finally, TruB1 suppressed cell proliferation, which was mediated in part by let-7. Altogether, we reveal an unexpected function for TruB1 in promoting let-7 maturation.

The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features

“…METTL16 and NSUN2 both target similar types of ncRNAs, such as vault RNAs, Y RNAs, U6 snRNA and lncRNAs ( 44 , 58 , 59 ). HITS-CLIP analysis of TRUB1 revealed binding to several classes of ncRNAs, but the extent of overlap with METTL16 RNA targets remained unknown as the analysis focused mainly on pri-miRNAs and tRNAs ( 60 ). Future studies will address whether the potential interactions between these different modifiers detected by BioID result from their activity on the same RNA molecule or whether they localize to specific nuclear foci that are formed to facilitate RNA processing.…”

Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods

“…The STRING analysis here reveals that PPRC1 interacts with TRUB1 (Figure 2), a synthase that catalyzes the pseudouridylation of mRNAs [126]. In 2020, Kurimoto et al [127] described the essential role of TRUB1 in the maturation of the miRNA let-7, an evolutionary conserved microRNA that mediates a post-transcriptional gene silencing regulating a wide range of biological processes, including development and differentiation [127]. The authors proposed that TRUB1 acts as a suppressor of cell proliferation, and therefore as a tumor suppressor, which is mediated in part by let-7 [127].…”

“…In 2020, Kurimoto et al [127] described the essential role of TRUB1 in the maturation of the miRNA let-7, an evolutionary conserved microRNA that mediates a post-transcriptional gene silencing regulating a wide range of biological processes, including development and differentiation [127]. The authors proposed that TRUB1 acts as a suppressor of cell proliferation, and therefore as a tumor suppressor, which is mediated in part by let-7 [127]. The STRING analysis also revealed that PPRC1 interacts with NOP56 and DKC1.…”

Relevance of 2′-O-Methylation and Pseudouridylation for the Malignant Melanoma

“…The pseudouridylation of different human RNA species is mediated by different pseudouridine synthases, such as pseudouridine synthase (PUS) 1, TruB pseudouridine synthase 2 (TRUB2), TRUB1, PUS3, PUS4, RNA pseudouridine synthase D3 (RPUSD3), RPUSD4, PUS7, pseudouridine synthase 7 like (PUS7L), PUS10 and DKC1 [ 28 ]. From these candidates, TRUB1 has been recently reported to modulate the stability of hsa-let-7 [ 51 ]. However, it is noteworthy that the actual list of enzymes involved in 2′-O-methylation and pseudouridylation of miRs might be incomplete.…”