N6-methyladenosine (m6A) is the most abundant internal chemical modification of mRNA in eukaryotes. m6A is deposited co-transcriptionally by the METTL3/METTL14 writer complex onto adenosines in a 5'-DRACH-3' sequence context (D = A/G/U, R = A/G, H = A/C/U), removed by demethylase erasers (FTO, ALKBH5), and recognised by reader proteins of the YTH and IGF2BP families. m6A regulates pre-mRNA splicing, nuclear export, mRNA decay, translation, and X-chromosome inactivation, and is increasingly implicated in development, immunity and cancer.
This track shows the high-confidence base-resolution m6A sites collected by m6A-Atlas v2.0 for the human genome. Each item marks a single A nucleotide that was independently identified by one or more base-resolution m6A sequencing technologies in one or more cell lines or tissues.
Each item is a single-base annotation at the modified A. Items are colored by the genomic region in which the site falls:
The score (0–1000, also used to shade items in pack mode) reflects the breadth of evidence: 150 points per supporting technique plus 30 points per additional supporting cell line, capped at 1000.
Filters are provided for the genomic region, the supporting detection technique(s), the supporting cell line / tissue, the host gene biotype, and for the minimum number of supporting techniques and cell lines.
The detail page links out to the corresponding m6A-Atlas entry, which provides the per-study evidence in a richer format.
m6A-Atlas v2.0 aggregates base-resolution m6A sites identified by 13 sequencing technologies (miCLIP, miCLIP2, meCLIP, m6ACE, m6A-CLIP-seq, PA-m6A-seq, m6A-REF-seq, MAZTER-seq, DART-seq, m6A-SAC-seq, m6A-label-seq, m6A-seq with improved protocol, and a single-cell adaptation), as reported in the original publications. Reads were processed with each technology's recommended pipeline, and only sites that pass technology-specific quality thresholds (the "reliable" / "high" tier) were retained. Each site is annotated with the supporting GEO study, technique, species, cell line and treatment, the surrounding 101 nt sequence context, the host gene (Ensembl), the genomic region, and the number of overlapping RNA-binding-protein binding sites, microRNA targets, splice sites and SNPs collected by the m6A-Atlas team. See Liang et al. 2024 for the full analysis pipeline.
For this track, the human (hg38) high-confidence file hg38_CL_Tech.txt.gz was downloaded from http://rnamd.org/m6a/download/high/hg38/hg38_CL_Tech.txt.gz. The 1-based single-base coordinates were converted to BED 0-based half-open, the per-study evidence was kept verbatim, the cell-line and technique lists were comma-separated, and a link to the m6A-Atlas detail page was added. The conversion script and autoSql definition are in the kent/src/hg/makeDb/scripts/rnaMod directory; the build steps are documented in kent/src/hg/makeDb/doc/hg38/rnaMod.txt. All 427,760 input rows from the source file were retained; no records were dropped during conversion.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our JSON API, track=m6aAtlas.
For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called m6aAtlas.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/rnaMod/m6aAtlas.bb -chrom=chr21 -start=0 -end=100000000 stdout
The original annotation source data can be downloaded from http://rnamd.org/m6a/download.php.
Thanks to Zhanmin Liang, Kunqi Chen, Jia Meng and the m6A-Atlas team for making the v2.0 dataset publicly available.
Liang Z, Ye H, Ma J, Wei Z, Wang Y, Zhang Y, Huang D, Song B, Meng J, Rigden DJ et al. m6A-Atlas v2.0: updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species. Nucleic Acids Res. 2024 Jan 5;52(D1):D194-D202. PMID: 37587690; PMC: PMC10768109