Extended Data Figure 3: Metagene analyses of human m1A peaks. | Nature

Extended Data Figure 3: Metagene analyses of human m1A peaks.

From: The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

Extended Data Figure 3

a, Metagene profiles demonstrating sequence coverage along a normalized gene transcript. Sequence reads of m1A immunoprecipitation and input in HeLa cells are indicated in blue and orange, respectively. bd, Metagene profiles of m1A peak distribution in a non-normalized window centred on the AUG start codon (b), extending downstream from the transcription start site (TSS) (c) and centred on the stop codon (d), in the indicated human cell types. e, Metagene profiles comparing the distribution of m1A peaks (blue) to that of negative peaks (black) along a normalized transcript composed of three rescaled non-overlapping segments illustrated below, in HeLa cells. f, Table demonstrating m1A peak enrichment in growing windows centred on the AUG start codon in HeLa cells. Enrichment is calculated as number of peaks in the window divided by window size (nucleotides). g, Table summarizing the overlap between m6A and m1A peaks in HepG2, HEK293 and WT mESCs. m6A peaks are sourced from Dominissini et al.1, Linder et al.67 and Geula et al.42, respectively. m1A peaks are from the current study. h, i, Metagene profiles of m1A peak distribution in a non-normalized window centred on the AUG codon (h) and extending downstream from the TSS (i). Peaks are sorted by the exon containing the AUG codon and the length of the first exon, respectively. j, Metagene profiles of m1A peak distribution in a non-normalized window centered on the nearest splice site. Peaks are sorted by the exon containing the AUG codon in that gene. k, m1A-induced reverse transcription (RT) arrests produce typical m1A peaks characterized by a central region of reduced coverage with a local minimum (m1A trough) Examples are shown. l, m1A-to-m6A rearrangement results in a reduced number of identified m1A troughs. Higher rates of rearrangement further reduce the number of identified m1A troughs (right panel). Example is shown (left panel). m, Metagene profile of m1A trough distribution along a normalized transcript composed of three rescaled non-overlapping segments illustrated below, in HepG2 cells. n, Metagene profile of m1A trough distribution in a non-normalized window centred on the AUG start codon in HepG2 cells. o, Metagene profile of m1A trough distribution along a normalized transcript in HepG2 cells. p, Metagene profile of m1A trough distribution in a non-normalized window centred on the nearest splice site in HepG2 cells. q, Pie chart presenting the fraction of m1A troughs in each of three non-overlapping transcript segments (5′ UTR, CDS and 3'UTR) in HepG2 cells. r, MEME motifs identified in 100-nucleotide windows centred on m1A troughs that lie within the AUG start codon window (±150 nucleotides) in HepG2 cells.

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