Fig. 5: paRNA-DNA interaction in human brain cells revealed by MUSIC data.

a A diagram showing RNA-DNA interaction at single-cell level in MUSIC data using cell barcodes (CB) and molecular barcodes (MB). CB is shared by all molecules in one cell, and MB is shared by all molecules in one molecular complex. b An UpSet plot showing paRNAs and their numbers (to the left) in different cell types detected by MUSIC from Normal brain. c A dotplot showing the average expression of the top five AD-upregulated paRNAs in MUSIC data. Ex: Excitatory neurons. In: Inhibitory neurons. Ast: Astrocyte. Mic: Microglia. Oli: Oligodendrocyte. Opc: Oligodendrocyte progenitor cell. d A barplot showing the numbers of differentially expressed genes seen after MAPT-paRNA KD that form RNA-DNA interactions with MAPT-paRNA in the Ex neurons. P value: Fisher’s exact test. e A barplot from permutation test showing the observed contact strength between MAPT-paRNA and its true 62 target genes (red arrow to the right) versus contact strength between MAPT-paRNA and 1000 sets of randomly selected 62 genes. f A barplot showing the number of paRNAs detected by MUSIC data in Ex neurons and the subset that show AD-deregulation in bulk RNA-seq data in Fig. 2. g A boxplot showing the RNA-DNA contact strength between the two groups of paRNAs and synaptic genes in Ex: AD-deregulated paRNAs (n = 47 in panel f), and non-AD-deregulated paRNAs (n = 346). P value: two-tailed non-parametric Wilcoxon–Mann–Whitney test. Boxplots indicate the interquartile range with the central line representing the median, and the vertical lines extending to the extreme values in the group. h A heatmap showing the RNA-DNA contact strength between AD-deregulated paRNAs and a single MEF2C gene detected in Ex and Ast, respectively.