Dynamic regulation and key roles of ribonucleic acid methylation

Abstract

Ribonucleic acid (RNA) methylation is the most abundant modification in biological systems, accounting for 60% of all RNA modifications, and affects multiple aspects of RNA (including mRNAs, tRNAs, rRNAs, microRNAs, and long non-coding RNAs). Dysregulation of RNA methylation causes many developmental diseases through various mechanisms mediated by N ⁶-methyladenosine (m⁶A), 5-methylcytosine (m⁵C), N ¹-methyladenosine (m¹A), 5-hydroxymethylcytosine (hm⁵C), and pseudouridine (Ψ). The emerging tools of RNA methylation can be used as diagnostic, preventive, and therapeutic markers. Here, we review the accumulated discoveries to date regarding the biological function and dynamic regulation of RNA methylation/modification, as well as the most popularly used techniques applied for profiling RNA epitranscriptome, to provide new ideas for growth and development.

Keywords: 5-hydroxymethylcytosine; 5-methylcytosine; N1-methyladenosine; N6-methyladenosine; RNA methylation; pseudouridine.

FIGURE 1

Structure and location of representative RNA post-transcriptional modifications. The chemical properties of RNA modifications (top). The known sites (bottom) of m⁶A, m¹A, m⁵C, and Ψ modification on mRNA.

FIGURE 2

Regulatory roles of m⁶A effector proteins. The m⁶A effectors, including writer proteins (i.e., m6A methyltransferase complex: core subunits METTL3 and METTL14 and additional adaptors proteins including WTAP, ZC3H13, VIRMA, METTL16, RBM15/15B, HAKAI, and KIAA1429); eraser proteins (i.e., RNA demethylases: FTO and ALKBH5), and reader (three classes of reader proteins: ➀ YTH-domain-containing proteins, including YTHDC1, YTHDC2, YTHDF1, YTHDF2, and YTHDF3; ➁ proteins favoring RNA-binding events, including HNRNPA2B1, HNRNPC, and HNRNPG; ➂ RNA binding proteins, including eIF3, IGF2BP1, IGF2BP2, and IGF2BP3). With the development of RNA modification detection technology, m⁶A modifications have been determined to functionally regulate the transcriptome of eukaryotes and processes, such as mRNA stability, splicing, nucleation, localization, and translation.

FIGURE 3

The reaction mechanism of a typical m⁵C-RNA cytosine methyltransferase [m(5)C-RMTs, in blue]. M⁵C, formed by the methylation of carbon 5 of cytosine.

FIGURE 4

Ten-eleven translocation (Tet)-catalyzed formation of hm⁵C in RNA. The Tet family of Fe(II)- and 2-oxoglutarate-dependent dioxygenases can induce the oxidation of m⁵C to yield hm⁵C.

FIGURE 5

Isomerization reaction of uridine into pseudouridine (Ψ). ψ is formed by the sequence-specific isomerization of uracil (U).

FIGURE 6

m⁶A depletion by METTL3/14 gene knockdown can promote the proliferation of neural stem cells and lead to prolonged cell cycle progression and maintenance of radial glial cells. IPC, intermediate progenitor cells.

FIGURE 7

The m⁶A methyltransferase METTL16 binds U6 snRNA. m⁶A typically locates at a DRACH motif, where D denotes A, G, or U; R denotes A or G; and H denotes A, C, or U.

FIGURE 8

Zc3h13 modulates RNA m⁶A methylation in the nucleus. Zc3h13 anchors WTAP, Virilizer, and Hakai in the nucleus to facilitate m⁶A methylation and to regulate mESC self-renewal. Upon Zc3h13 knockdown, a great majority of WTAP, Virilizer, and Hakai translocate to the cytoplasm to inhibit m⁶A methylation.

FIGURE 9

Regulation and function of RNA m⁵C methylation. C5-methylcytidine (m⁵C) is a common modification in (A) tRNAs and (B) other non-coding RNAs (ncRNAs). NSUN family enzymes (NSUN2, NSUN4) and DNMT2 have been identified as m5C writers, while ALYREF and YBX1 have been identified as m5C readers.