Recent advances in methylation modifications of microRNA

Abstract

microRNAs (miRNAs) are short single-stranded non-coding RNAs between 21 and 25 nt in length in eukaryotic organisms, which control post-transcriptional gene expression. Through complementary base pairing, miRNAs generally bind to their target messenger RNAs and repress protein production by destabilizing the messenger RNA and translational silencing. They regulate almost all life activities, such as cell proliferation, differentiation, apoptosis, tumorigenesis, and host-pathogen interactions. Methylation modification is the most common RNA modification in eukaryotes. miRNA methylation exists in different types, mainly N⁶-methyladenosine, 5-methylcytosine, and 7-methylguanine, which can change the expression level and biological mode of action of miRNAs and improve the activity of regulating gene expression in a very fine-tuned way with flexibility. In this review, we will summarize the recent findings concerning methylation modifications of miRNA, focusing on their biogenesis and the potential role of miRNA fate and functions.

Keywords: Methylation modification; m5C modification; m6A modification; m7G modification; miRNA.

Figure 1

Biosynthesis pathway and function of miRNA. The pri-miRNA is transcribed by RNA polymerase II (Pol II) and cleaved by Drosha/DGCR8 microprocessor complex in the nucleus, which releases pre-miRNA. Then, the pre-miRNA is exported to the cytoplasm by the Exportin5-RanGTP complex. In the cytoplasm, Dicer cleaves the terminal loop of the pre-miRNA to produce the miRNA duplex. The latter is unwound to produce the ∼22-nt-long mature miRNA. Subsequently, the mature miRNA's functional strand is incorporated with Argonaute (AGO) proteins to form the miRISC, playing a role in mRNA decay or translation inhibition. DGCR8, DiGeorge syndrome chromosomal region 8; miRISC, miRNA-induced silencing complex.

Figure 2

Dynamic reversible process of m⁵C, m⁶A, and m⁷G modification of RNA. Writers, erasers, and readers catalyze those modifications. (A) The sixth N position of adenylate can be methylated by m⁶A writers to form m⁶A. Writers include METTL3/14/16, WTAP, RBM15/15b, VIRMA, and ZC3H13. Erasers are proteins with demethylase activity and include FTO and ALKBH5. Readers are proteins that perform a biological function by recognizing m⁶A modifications, including YTHDF1–3, YTHDC1/2, eIF3, IGF2BPs, ELAVL1, Prrc2a, and RBM33. (B) The fifth C position of cytosine can be methylated by m⁵C writers to form m⁵C. Writers include NSUN and DNMT2. Erasers include TET1/2/3. Readers include ALYREF and YBX1. (C) m⁷G is a positively charged modification by METTL1, a methylated transcriptase, that co-transcriptionally modifies the methyl group at the seventh N position of the guanine. Reader includes QKI. WTAP, Wilms tumor 1 associated protein; METTL1/3/14/16, methyltransferase like 1/3/14/16; RBM15/15b, RNA binding motif protein 15/15b; RBM33, RNA binding motif protein 33; VIRMA, vir like m⁶A methyltransferase associated; ZC3H13, zinc finger CCCH-type containing protein 13; FTO, fat mass and obesity-associated protein; ALKBH5, alkB homolog 5; YTHDC1/2, YTH domain-containing 1/2; YTHDF1–3, YTH domain-containing family 1–3; ELAVL1, ELAV like RNA binding protein 1; Prrc2a, proline-rich helix-coil 2 A; NSUN, NOL1/NOP2/SUN; DNMT2, DNA methyltransferase-2; TET1/2/3, ten-eleven translocation 1/2/3; ALYREF, Aly/REF export factor; YBX1, Y-box binding protein 1; QKI, Quaking protein.

Figure 3

Biological functions of miRNA m⁶A modifications. (A) In the nucleus, m⁶A modification contributes to recruiting DGCR8 to target pri-miRNA, thus facilitating the cleavage of pri-miRNA to pre-miRNA by DGCR8 and the intranuclear enzyme Drosha. (B) In the cytoplasm, m⁶A modifications on pre-miRNAs are recognized by YTHDF2, which then recruits the AGO2 protein to help pre-miRNAs to shear and promote their maturation. (C) The m⁶A modification on miRNA resulted in significant structural changes of miRISC complexes, thereby repressing the target mRNA recognition efficiency. DGCR8, DiGeorge syndrome chromosomal region 8; YTHDF2, YTH domain-containing family 2; AGO2, Argonaute 2; miRISC, miRNA-induced silencing complex.