Origins of De Novo Genes in Human and Chimpanzee.

Jorge Ruiz-Orera,M.Mar Albà,Ivanela Kondova,Tomàs Marqués-Bonet,Jessica Hernandez-Rodriguez,Eduard Sabidó,Cristina Chiva,Ronald Bontrop,James Noonan

doi:10.1371/journal.pgen.1005721

Abstract

The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species—human, chimpanzee, macaque, and mouse—and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.

Highlights

IntroductionIn recent years another important mechanism for the birth of new functional genes has been discovered- de novo gene emergence [5,6,7]
For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species
How have these genes originated? The advent of massively parallel RNA sequencing (RNA-Seq) has provided new clues to this question, with the discovery of an unexpectedly high number of transcripts that do not correspond to typical protein-coding genes, and which could serve as a substrate for this

Summary

Introduction

In recent years another important mechanism for the birth of new functional genes has been discovered- de novo gene emergence [5,6,7]. Genes that have recently evolved de novo are characterized by their lack of homologous genes in other species and, contrary to duplicated genes, they can evolve without the limitations which constrain sequences that have high similarity to a pre-existing gene [15]. Despite their recent origin, it has been shown that de novo Drosophila genes can quickly become functionally important [13,16]

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Conclusion