Table 1.

The general characteristics of main RNA modification types

Type	Contribution	Class	Regulator	Function	Ref.
m6A	mRNA, rRNA, snRNA, snoRNA, miRNA, lncRNA, circRNA, eRNA	writer	METTL3	Catalyzes most of the m6A modifications via forming methyltransferase complex (MTC) with METTL14	34
			METTL14	Provides structural support in MTC	35
			METTL16	Catalyzes m6A in U6 snRNA	40
		eraser	FTO	Removes m6A/m6Am/m1A modifications	44,45
			ALKBH5	Demethylates m6A modification exclusively	50
		reader	YTHDF1	Stabilizes transcripts and initiates translation	56,57
			YTHDF2	Promotes degradation	56,57
			YTHDF3	Facilitates translation and degradation	56,57
			YTHDC1	Mediates RNA splicing, nuclear export and degradation	54
			YTHDC2	Promotes translation efficacy and decay	55
			IGF2BP1/2/3	Stabilizes transcripts and facilitates translation	58,59
			HNRNPs	Mediate splicing of pre-mRNAs and/or pri-miRNAs	60
m6Am	mRNA, snRNA	writer	PCIF1	Catalyzes m6Am next to the 5′ cap of mRNAs and in snRNAs	77
			METTL4	Catalyzes m6Am at position 30 in human U2 snRNA	80
		eraser	FTO	Removes m6A/m6Am/m1A modifications	49
m1A	tRNA, rRNA, lncRNA, and mRNA	writer	TRMT61B	Catalyzes mA at positions 58 (m1A58)	92
			TRMT10C	Catalyzes mA at positions 9 (m1A9)	92,93
			TRMT6/61A	Catalyzes m1A in tRNA at A58 and mRNA	94
			TRMT61B	Mediates m1A in mitochondrial 16S rRNA	95
		eraser	ALKBH1	Catalyzes demethylation of most m1A in cyto-tRNAs	97
			ALKBH3	Demethylates m1A in both tRNAs and mRNAs	98,99
			ALKBH7	Demethylates m1A within mitochondrial Leu1 pre-tRNA regions	100
			FTO	Demethylates m1A in tRNA	49
		reader	YTHDF1/2/3 YTHDC1	Mediates stabilization, degradation, splicing, translation	101,102
m5C		writer	NSUN1	Catalyzes m5C at position 4413 of 28S rRNA	114
			NSUN5	Catalyzes m5C at position 3761 of 28S rRNA	115
			NSUN2	Methylates C34, C40, C48, C49, and C50 in several tRNAs	116
			NSUN6	Methylates C72 in particular tRNAs	117
			DNMT2	Methylates C38 in particular tRNAs	118
			NSUN3	Catalyzes m5C in mitochondrial tRNA	119
			NSUN4	Catalyzes m5C in 12S rRNA	120
		eraser	ALKBH1	Demethylates m5C at position 34 of cytoplasmic and mitochondrial tRNA	126,127
			TET1/2/3	Catalyzes first step of m5C demethylation	128
		reader	ALYREF	Promotes the nuclear export of m5C-modified rRNAs	129
			YTHDF2	Modulates the maturation of m5C-modified rRNAs	130
ac4C	mRNA, tRNA, rRNA	writer	NAT10	THUMPD1 and snoRNP are necessary assistants for modifying tRNA and 18S rRNA, respectively	141,140,141
m7G	mRNA, tRNA, rRNA, miRNA	writer	METTL1	Forms complex with WDR4 to catalyze m7G on tRNA, miRNA, and mRNA	147
			RNMT	Catalyzes m7G on recapped mRNAs, cooperated with RAM	149
			WBSCR22	methylate G1639 in human 18S rRNA, cooperated with TRMT112	150
			TGS1	Catalyzes hypermethylation of m7G caps into m2,2,7G in snRNAs and snoRNAs	151
		reader	eIF4E, CBC	recognizes m7G cap and further affect RNA maturation, nuclear export, and translation	152
Ψ		writer	DKC1	Forms a complex with box H/ACA snRNA to pseudouridylates rRNA	160
A-to-I	Pre-mRNA, pri-miRNA	writer	ADAR1-3	ADAR1 and ADAR2 could catalyze all known A-to-I editing events, while ADAR3 has no deaminase activity	186