Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates

Abstract

Human and chimpanzee genomes are almost identical, yet humans express higher brain capabilities. Deciphering the basis for this superiority is a long sought-after challenge. Adenosine-to-inosine (A-to-I) RNA editing is a widespread modification of the transcriptome. The editing level in humans is significantly higher compared with nonprimates, due to exceptional editing within the primate-specific Alu sequences, but the global editing level of nonhuman primates has not been studied so far. Here we report the sequencing of transcribed Alu sequences in humans, chimpanzees, and rhesus monkeys. We found that, on average, the editing level in the transcripts analyzed is higher in human brain compared with nonhuman primates, even where the genomic Alu structure is unmodified. Correlated editing is observed for pairs and triplets of specific adenosines along the Alu sequences. Moreover, new editable species-specific Alu insertions, subsequent to the human-chimpanzee split, are significantly enriched in genes related to neuronal functions and neurological diseases. The enhanced editing level in the human brain and the association with neuronal functions both hint at the possible contribution of A-to-I editing to the development of higher brain function. We show here that combinatorial editing is the most significant contributor to the transcriptome repertoire and suggest that Alu editing adapted by natural selection may therefore serve as an alternate information mechanism based on the binary A/I code.

Fig. 1.

Higher editing level in human vs. nonhuman primates. (A) Editing levels of 75 sites in six transcripts originating from cerebellum tissues of four humans, two chimpanzees, and two rhesus monkeys were quantified after PCR amplification using the DSgene program. Average editing values were normalized (Z-score) and colored accordingly with blue-yellow gradient using the Spotfire program (Tibco). (B) Editing level per site for humans, chimpanzees, and rhesus monkeys. The human editing sites are ordered in decreasing editing levels, and the nonhuman primate editing sites are aligned, accordingly. (C) Editing levels in cerebellum tissues of eight individual primates: a total of the resulting editing level quantification in the six tested transcripts are plotted in four human, two chimpanzee, and two rhesus individuals where the bar size is proportional to the total of the editing levels in all tested sites.

Fig. 2.

Possible effects of Alu architecture alterations on RNA editing. Schematic representation of the genomic Alu elements’ location and orientation: Alu elements are marked as arrow-shaped boxes in the human (blue) and monkey (red) genomes. Alterations between the species are indicated in orange. (A) Minor alteration in Alu sequence between the species. (B) Inversion of one of the Alu sequences along primate evolution. (C) Deletion of Alu element along evolution. (D) Insertion of additional Alu sequence along evolution.

Fig. 3.

Analysis of newly inserted Alus. Number of common human and chimpanzee genes showing new (independent) Alu element insertions. Among the 165 shared genes representing new independent Alu insertions in the human and chimpanzee, 115 are neurological function and neurological disease-associated genes.

Fig. 4.

Combinatorial behavior and editing site dependencies. (A) Number of different variants as a function of the number of 454 sequencing reads. None of the graphs shows signs of saturation, indicating that the repertoire of different variants is not exhausted. The ratio of the number of different transcripts to the one expected in the absence of site–site correlations (excluding correlations resulting from the overall transcript editing level) is also shown. A ratio significantly less than 1 indicates the existence of significant dependencies between sites (see Dataset S5). (B) Number of significantly correlated and (C) anticorrelated editing-site pairs, as a function of the nucleotide distance between the sites. (D) Number of significantly triplet-correlated and (E) anticorrelated sites as a function of the nucleotide distance spanned by the triplet.