Fig. 4: Detection and mapping of RNA base modifications.

a Representation of the synthetic hairpin constructed for epigenetic detection on RNA (see Supplementary Fig. 1 for more details). The red line represents RNA whereas black lines depict DNA. The Y shape adapter, to attach the hairpin on MyOne streptavidin bead via a biotin (green circle), as well as the loop are colored in purple. The binding position histogram of specific antibodies, as well as a reference oligonucleotide mix binding on a single hairpin is shown below. The reference oligonucleotides peaks are marked with an asterisk (*), and are used for alignment. The antibody binding positions are shown by the red lines. The last histogram represents the reference oligonucleotide binding positions that correspond to the same position as the modification. b Venn diagram showing the overlap between three different m⁶A antibody clones (top). Below, the Venn diagram shows the overlap between non-specific binding identified by m⁵C antibody (ICC) at the position of m⁶A modification, and the binding positions identified by at least two out of three m⁶A antibodies. c Boxplot showing the distance of binding between antibody and the reference oligonucleotides is base pair resolution for all antibodies tested. Whisker boxes represent 50% of the points with the average as a line within the box and the median as a cross. d Table showing the sensitivity and the specificity of all three m⁶A antibodies and the m⁵C antibody tested. For the combined analysis of m⁶A antibodies, a binding position was considered as such if it is recognized by at least two out of the three antibodies tested.