Abstract
Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.
Highlights
Over the last decade the way we look at the human and other genomes has changed in a striking way
Analyzed retrocopies were downloaded from a RetrogeneDB database, a repository of retrotransposed genes identified in 62 animal and 37 plant species [33]
As for the human genome, RetrogeneDB includes 4611 retrocopies from which 4384 are annotated as known pseudogene, 106 have a status of known protein-coding genes and 121 as novel
Summary
Over the last decade the way we look at the human and other genomes has changed in a striking way. The estimated fraction of the human genome derived from retroposition has increased to over 70% [1]. It has been established that the majority of human RNA transcripts do not encode proteins and that non-coding RNAs regulate cell functions. These discoveries strongly support an RNA-centric view of evolution in which phenotypic diversity arises through extensive RNA processing and an RNA-directed rewriting of DNA. One of these processes, which plays a fundamental role in evolution, is the birth of new genes via retroposition
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