A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

Abstract

To understand whether any human-specific new genes may be associated with human brain functions, we computationally screened the genetic vulnerable factors identified through Genome-Wide Association Studies and linkage analyses of nicotine addiction and found one human-specific de novo protein-coding gene, FLJ33706 (alternative gene symbol C20orf203). Cross-species analysis revealed interesting evolutionary paths of how this gene had originated from noncoding DNA sequences: insertion of repeat elements especially Alu contributed to the formation of the first coding exon and six standard splice junctions on the branch leading to humans and chimpanzees, and two subsequent substitutions in the human lineage escaped two stop codons and created an open reading frame of 194 amino acids. We experimentally verified FLJ33706's mRNA and protein expression in the brain. Real-Time PCR in multiple tissues demonstrated that FLJ33706 was most abundantly expressed in brain. Human polymorphism data suggested that FLJ33706 encodes a protein under purifying selection. A specifically designed antibody detected its protein expression across human cortex, cerebellum and midbrain. Immunohistochemistry study in normal human brain cortex revealed the localization of FLJ33706 protein in neurons. Elevated expressions of FLJ33706 were detected in Alzheimer's brain samples, suggesting the role of this novel gene in human-specific pathogenesis of Alzheimer's disease. FLJ33706 provided the strongest evidence so far that human-specific de novo genes can have protein-coding potential and differential protein expression, and be involved in human brain functions.

Author Summary

For decades, gene duplication, retrotranspositions and gene fusions were believed to be major ways to increase gene number. All involve “mother” genes as the “building blocks” for new genes. However, several recently identified “motherless” genes challenged the idea in that some proteins might have emerged de novo from ancestral non-coding DNAs. Did any such genes emerge in human after the divergence from chimpanzee? If yes, such genes might help understand what makes us human. Here we report the first experimentally verified case of a human-specific protein-coding gene, FLJ33706 (alternative gene symbol C20orf203), that originated de novo since the divergence of human and chimpanzee. FLJ33706 was formed by the insertion of repeat elements, especially Alu sequences, that contributed to the formation of the first coding exon and six standard splice junctions, followed by two human-specific substitutions that escaped stop codons. The functional protein-coding features of the FLJ33706 gene are supported by population genetics, transcriptome profiling, Western-blot and immunohistochemistry assays. Data suggest that FLJ33706 may be involved in nicotine addiction and Alzheimer's disease. FLJ33706 provided the strongest evidence so far that human-specific de novo genes can have protein-coding potential and be involved in human brain functions.