Summary of methods for mapping DNA modifications.

Modifications	Methods	Treatment	Resolution	Principles of sequencing	Ref.
5mC, 5hmC	BS-seq	Bisulfite treatment	Single-base resolution	C, 5fC and 5caC undergo deamination and all of them are read as T, while 5mC and 5hmC are resistant to deamination and are read as C.	166
	TAPS	Oxidation of 5mC, 5hmC and 5fC by TET proteins; reduction of 5caC by pyridine borane		TET oxidizes 5mC, 5hmC and 5fC to 5caC, then pyridine borane reduces 5caC to DHU, which is read as T in PCR and thereby realize the C-to-T conversion of 5mC and 5hmC.	182
	EM-seq	Oxidation of 5mC by TET2 and glycosylation of 5hmC by β-GT; deamination of C by APOBEC3A		TET2 oxidation and β-GT glycosylation protect 5mC, 5hmC and 5fC from APOBEC3A deamination; only C is converted to U, which is read as T in sequencing. 5mC, 5hmC and 5fC are read as C.	204
5mC	TAPSβ	Glycosylation of 5hmC by β-GT; TET oxidation and pyridine borane reduction of 5mC	Single-base resolution	β-GT glycosylation protects 5hmC from TET oxidation and pyridine borane reduction; only 5mC is converted to DHU, which is read as T in sequencing.	182
5hmC	oxBS-seq	Oxidation of 5hmC by KRuO4	Single-base resolution	KRuO4 oxidizes 5hmC to 5fC, which is read as T in BS-seq, while 5mC is read as C.	167
	TAB-seq	Glycosylation of 5hmC by β-GT and oxidation of 5mC by TET proteins		Glycosylation of 5hmC to 5gmC by β-GT; TET oxidizes 5mC to 5fC and 5caC, both of which are read as T in BS-seq, while the original 5hmC is read as C.	168
	hmC-CATCH	Labeling of 5fC by EtONH2; oxidation of 5hmC by K2RuO4 and labeling by 1,3-indandione (AI)		Protection of 5fC by EtONH2; K2RuO4 oxidizes 5hmC to 5fC followed by AI labeling, which induces a C-to-T transition in sequencing.	178
	CAM-Seq	KRuO4 oxidation and azi-BP labeling of 5hmC		Protection of 5fC by hydroxylamine; KRuO4 oxidizes 5hmC to 5fC followed by azi-BP labeling, which induces C-to-T conversion in sequencing.	180
	CAPS	Oxidation of 5hmC by KRuO4 and reduction by pyridine borane		KRuO4 oxidizes 5hmC to 5fC, then is reduced to DHU by pyridine borane. DHU is read as T in sequencing.	182
	hmC-seq	Oxidation of 5hmC by peroxotungstate		Peroxotungstate converts 5hmC to trihydroxylated thymine (thT), leading to a C-to-T transition in polymerase extension.	181
	AMD-seq, ACE-seq	Glycosylation of 5hmC by β-GT; deamination of C by APOBEC3A		β-GT glycosylation protects 5hmC from APOBEC3A deamination and 5gmC is read as C; C and 5mC are read as T.	202 and 203
	hmC-seq	Glycosylation of 5hmC by β-GT and precipitation by JBP1	Genome-wide	β-GT converts 5hmC to 5gmC that can be pulled down by J-binding protein 1 coupled to magnetic beads.	195
	nano-hmC-Seal	Glycosylation of 5hmC by β-GT		Labeling of 5hmC to 6-N3-β-glucosyl-5hmC by β-GT, then a biotin tag is installed onto the azido group for pull down using click chemistry.	197
5fC	redBS-seq	Reduction of 5fC by NaBH4	Single-base resolution	NaBH4 reduces 5fC to 5hmC, which is converted to CMS by bisulfite treatment. The 5fC site is identified by comparing the output of redBS-seq (where 5fC is read as C) with that of BS-seq (where 5fC is read as T).	170
	fCAB-seq	Conversion of 5fC to oxime by EtONH2		EtONH2 converts 5fC to oxime, which resists deamination by bisulfite treatment. The 5fC site is identified by comparing the output of fCAB-seq (where 5fC is read as C) with that of BS-seq (where 5fC is read as T).	171
	fC-CET	Labeling of 5fC by 1,3-indandione (AI)		Labeling of 5fC by AI enables a subsequent C-to-T transition in PCR.	191
	CLEVER-seq	Labeling of 5fC by malononitrile		Labeling of 5fC by malononitrile induces a C-to-T conversion in sequencing.	192
	fC-seq	Labeling of 5fC by 2-(5-chlorobenzo[d] thiazol-2-yl)acetonitrile (CBAN) or azi-BP		CBAN or azi-BP reacts with 5fC to generate an intramolecular cyclization nucleobase, leading to a C-to-T conversion in polymerase extension.	142 and 193
	fC-seq	Labeling of 5fC by O-(biotinylcarbazoylmethyl) hydroxylamine (ARP)	Genome-wide	Labeling of 5fC by ARP to form a biotinylated 5fC, which can be enriched by streptavidin-coated magnetic beads and then sequenced.	160
5caC	CAB-seq	Labeling of 5caC by EDC-catalyzed xylene-based primary amine	Single-base resolution	Labeling of 5caC with xylene-based primary amine, which protects 5caC from deamination. The labeled 5caC is read as C in BS-seq.	172
	caMAB-seq	Reduction of 5fC by NaBH4; methylation of C by M.SssI enzyme		5fC is reduced to 5hmC by NaBH4; methylation of C by M.SssI. 5caC is sequenced as T in BS-seq, whereas C, 5mC, 5hmC and 5fC are read as C.	174
5fC, 5caC	MAB-seq	Methylation of C by M.SssI enzyme	Single-base resolution	Methylation of CpG by M.SssI protects unmodified C from bisulfite conversion to U. 5fC/5caC is read as T in sequencing.	175
4mC	4mC-TAB-seq	Oxidation of 5mC by TET proteins	Single-base resolution	Oxidation of 5mC to 5caC by TET proteins followed by bisulfite treatment; 5mC is read as thymine, while 4mC is read as cytosine in sequencing.	177
5hmU	hmU-seq	Oxidation of 5hmU by KRuO4	Single-base resolution	Oxidation of 5hmU to 5fU by KRuO4 induces a T-to-C base transition in polymerase extension.	179
	hmU-seq	Glycosylation of 5hmU by base J glucosyltransferase (J-GT)	Genome-wide	Labeling of 5hmU with N3-glucose by J-GT followed by adding biotin tag and enrichment with streptavidin-coupled beads.	199
5fU	fU-seq	Labeling of 5fU by azi-BIAN	Genome-wide	Azi-BIAN labeling of 5fU enables pull down of 5fU-containing DNA fragments for sequencing.	188
OG	OG-seq	Oxidation of OG by K2IrBr6	Genome-wide	K2IrBr6 oxidizes OG to a covalent adduct of a primary-amine-terminated biotin, allowing for enrichment and sequencing.	189
6mA	6mA-seq	Deamination of adenine by sodium nitrite (NaNO2)	Single-base resolution	NaNO2 deaminates unmethylated adenines to hypoxanthine bases, which are read as guanine by polymerase and reverse transcriptase. 6mA site resists deamination and is read as adenine.	194