Landscape of A-I RNA editing in mouse, pig, macaque, and human brains

Figures

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  Figure 1.. Genome-wide RNA editing landscape in macaque brain. (A) The pipeline of A-to-I RNA editing analysis. The 39 subregions are organized into 10 brain regions. The regions are as follows: ctx, cerebral cortex; hp, hippocampal formation; am, amygdala; bg, basal ganglia; hy, hypothalamus; th, thalamus; mb, midbrain; pm, pons and medulla; cb, cerebellum; and sc, spinal cord. (B) Proportions of A-I RNA editing sites within genic regions. The pie chart shows the proportion of unique sites and repetitive sites within the coding sequences (CDS). (C) Proportions of A-I RNA editing sites within repetitive regions. (D) Percentages of editing sites occurring in clusters (at least three sites within a 100-bp window) across intron, 5′ untranslated regions (UTR), 3′ UTR, and CDS. (E) Percentages of editing sites occurring in clusters in SINE/Alu and LINE/L1. (F-G) Nucleotide frequency in the flanking sequences (5 bp upstream and downstream) of the editing sites and randomly selected genomic “A” and “T” sites (F, sense strand; G, antisense strand).

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  Figure 2.. The macaque A-I recoding sites. (A) The number of nonsynonymous (recoding) and synonymous editing sites (pie chart), and distribution of types of amino acid changes (bar chart). (B) The top 20 genes harboring edited CDS residing sites. (C) The top GO terms associated with genes harboring recoding sites. (D) Heatmap showing the editing level of recoding editing sites located in gene encoding glutamate receptors. Gray represents a lack of coverage or no editing events detected based on our filter criteria. (E) Editing level of the I342M recoding site in GABRA3 across 10 brain regions. (F) Heatmap showing the editing level of recoding editing sites located in G protein-coupled serotonin receptor 2C (HTR2C). Gray represents a lack of coverage or no editing events detected based on our filter criteria.

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  Figure 3.. RNA editing profiles across brain regions. PCA based on editing levels (A) and gene expression (B) across 30 anatomically defined subregions. The 30 subregions are organized into 10 brain regions. The regions are as follows: ctx, cerebral cortex; hp, hippocampal formation; am, amygdala; bg, basal ganglia; hy, hypothalamus; th, thalamus; mb, midbrain; pm, pons and medulla; cb, cerebellum; and sc, spinal cord, represented by points of different colors. Different shapes of points represent the five broad functional brain regions. (C) The percentage of editing sites classified according to regional specificity. Region-enriched sites are characterized by an editing level surpassing that of any other region by at least 20% within a singular region. Group-enriched sites necessitate an editing level that is at least 20% greater in more than one but less than one-third of regions (two to three regions in this study), relative to any other region. Lastly, region-enhanced sites are identified by an editing level that exceeds the average across all regions by at least 20%. (D) Chord diagrams showing region-specific editing sites across 10 brain regions. (E) Global editing activities across…

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  Figure 4.. Conserved RNA editing in multiple mammals. (A) The number of RNA editing sites identified in mice, pigs, humans, and macaques. (B) The number of RNA editing sites conserved between three other mammals and humans, as well as the overlap among these three mammals. (C) The top result of GO enrichment analysis on genes harboring conserved RNA editing sites with Metascape. (D) The heatmap showing the editing level of the recoding sites in macaque that are conserved among the four species. Gray represents a lack of coverage or no editing events detected based on our filter criteria. (E) Mean expression levels of ADAR1, ADAR2, and ADAR3 in homologous brain regions across humans (primates), macaques (in-house), pigs, and mice. (F) Cross-species correlation of ADAR isozyme expression in homologous brain regions (Spearman; *P< .05, **P< .01, ***P < .001). (G) The density plot illustrates the distribution of RNA editing levels at conserved sites across three species. (H) Comparison of editing levels of conserved editing sites in the cerebral cortex of humans, macaques, and pigs. The numbers in the figure represent the number of sites in one species where RNA editing levels are higher than…

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  Figure 5.. RNA editing sites in primates. (A) Number of conserved sites in eight conserved regions (top). Comparisons of conserved editing sites across eight brain regions (bottom): cerebral cortex, hippocampal formation, amygdala, basal ganglia, hypothalamus, midbrain, cerebellum, and spinal cord. Species-biased sites were defined as those showing ≥20% editing level difference between species with statistical significance (Fisher’s exact test, FDR < 0.01 by Benjamini–Hochberg correction). (B) Editing level of human-biased H5R recoding site in RMND5B in primates. (C) Predicted dsRNA structures of the sequence flanking the RMND5B (H5R). (D) Editing level of KCNA1 (I400V) in each region. (E) Amino acid sequence within the S6 transmembrane domain across voltage-gated potassium channels with Ile400 highlighted in red. (F) Cartoon diagram of the pore domain in the predicted 3D structure of the Macaca fascicularis Kv1.1 voltage-gated K+ channel shown from the side, with the six identical subunits colored differently. PH, pore helix; SF, selectivity filter (right). Magnification showing Ile400 of the S6 segment and its distance to M370 and T371 of the pore in the adjacent helix, the two amino…