Fig. 6.

hnRNP A2/B1 does not specifically recognize m⁶A-modified RNA. a Surface representation of the environment around A₄ in 8mer RNA complex. b Surface representation of the environment around A₄ in 10mer RNA complex. c Surface representation of the canonical N⁶-methylated adenosine binding mode in HsYTHDC1. The aromatic cage is circled with yellow dashline. d ITC data of hnRNP A2/B1(12–195) with 8mer and 10mer RNA targets carried N⁶-methylated adenosine. e EMSA experiment shows the binding affinity of full-length hnRNP A2/B1 with 5′-FAM-labeled RNA substrates with or without m⁶A modification. Uncropped gel image is shown in Supplementary Fig. 7e. The data represent the mean of three independent experiments, with standard deviation (SD) values indicated by error bars. f YTHDC1 shows preferential binding to m⁶A sites in nuclear RNA compared to hnRNP A2/B1. For hnRNP A2/B1, the m⁶A-Seq reads that overlapped with each m⁶A site was plotted on the x-axis, and the HITS-CLIP reads that overlap with each site were plotted on the y-axis. A similar analysis was used to examine YTHDC1 binding at these m⁶A sites. miCLIP reads that overlapped with the m⁶A sites were plotted on the x-axis, and the YTHDC1 iCLIP reads that overlapped with the m⁶A sites were plotted on the y-axis. g YTHDC1-m⁶A tag cluster overlap. A Venn diagram indicating the cluster overlap is shown. Roughly, 43 and 56% of miCLIP tag clusters from total cellular RNA and poly(A) RNA showed a significant overlap with the YTHDC1 iCLIP clusters, respectively