Table 1.

A summary of mammalian 6mA mapping methods and the representative applications

Method	Strengths/limitations	Year/reference	Tissues/cell lines	Abundance	Motif	Enriched regions	Functions
6mA-DIP-seq	efficient and easy-to-use/large DNA input amount; low resolution; low sensitivity; not quantitative; high false-positive rate because of the non-specific binding	2017; Yao et al.30	mouse prefrontal cortex	37,937 gain-of-6mA regions and 21,974 loss-of-6mA regions upon stress	‐	intergenic and intronic regions	negatively correlates with neuronal gene expression
		2018; Xie et al.45	normal human astrocytes and human patient-derived glioma stem cells	7,282–17,263 peaks	GGAAT	heterochromatin	transcriptional silencing of oncogenic pathways
		2018; Xiao et al.32	human blood	21,129 high-confidence peaks	‐	exon-coding regions; mtDNA	‐
		2019; Kweon et al.34	mouse ES cells	4,922 peaks	AGAAGAGGA	Intergenic regions	triggering proteolysis of its cognate sensor proteins
		2020; Li et al.38	mouse ES cells to trophoblast cells	20,318 differentially increased peaks	‐	intergenic regions, such as LINE-1s	repressing SIDD-SATB1 interactions and regulating gene expression during trophoblast development
		2022; Chen et al.43	human breast cancer cells (MDA-MB-453)	17,294 high-confidence peaks	[G/C]AGG	introns, intergenic regions, enhancers, and upstream promoter regions	repressing the expression of cell cycle inhibitor genes
SMRT-seq/Nanopore sequencing/6mASCOPE	base resolution; quantitative/large DNA input amount; high false positive rate when the abundance of modification is low	2016; Wu et al.17	mouse TT2 ES cells	37,581 sites with Alkbh1 knockout	GAA; AATA	intergenic regions, young full-length LINE-1 transposon	repressing the expression of nearby genes
		2018; Zhu et al.31	Human lymphoblastoid cells (hLCLs)	‐	AG	promotors of young full-length LINE-1 transposon	‐
		2018; Xiao et al.32	Human lymphocytes (HX1)	881,240 sites	[G/C]AGG[C/T]	exon-coding regions; mtDNA	repressing tumorigenesis
		2019; Pacini et al.46	Human lymphoblastoid cell line (AK1); human hydatidiform cell lin (CHM1)	74,345 sites in CHM1 and 80,561 sites in AK1	AG/GA	introns, exons, in the 5’ UTR and near transcriptional start sites (TSSs)	‐
		2022; Cui et al.42	hepatocellular carcinoma (HCC)	500 ppm	AGG	intergenic and intronic regions	positively correlated with gene expression
		2022; Kong et al.26	HEK293T; human glioblastoma brain tissues; human peripheral blood mononuclear cells (PBMCs)	1; 2–3; 17 ppm	no reliable motif	not supporting the enrichment of 6mA in young L1 elements or mtDNA	‐
ChIP-exo/6mACE-seq	base resolution/large DNA input amount; low sensitivity; high false positive rate because of the non-specific binding	2018; Koh et al.33	HEK293T	14,000 sites	AATGG	young and active LINE and SINE subfamilies; mtDNA	destabilizing dsDNA and regulating mitochondrial function
		2020; Hao et al.40	HepG2	23 sites under normoxia; 34 sites under hypoxia (mtDNA only)	CTTATC	‐	repressing the transcription of mitochondrial genes
6mA-RE-seq/DA-6mA-seq	base resolution/limited motifs	2019; Li et al.35	mouse primary cortical neuron	2,033,704 + 306,207 GATC sites for extinction training group; 2,033,704 + 212,326 GATC sites for retention control group	‐	LINE1 elements	positively correlated with gene expression and the formation of fear extinction memory