Open questions in the study of de novo genes: what, how and why

Journal name:
Nature Reviews Genetics
Volume:
17,
Pages:
567–578
Year published:
DOI:
doi:10.1038/nrg.2016.78
Published online
Corrected online

Abstract

The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes.

At a glance

Figures

  1. A systematic approach to the classification of novel genes.
    Figure 1: A systematic approach to the classification of novel genes.

    This classification is based on tracing the evolution of a locus to the most recent common ancestor in which it can be inferred that there was no expressed open reading frame (ORF) at the orthologous location, and then inspecting the evolutionary steps in the origin of the gene. This requires abundant, closely related, high-quality genomes. Evidence of the presence of a translated ORF, even a relatively short one, can be sought through ribosome protection assays33, 121, 122. The defining characteristic of a de novo gene is that it evolved from previously non-coding sequence; therefore, it must be possible to identify that sequence otherwise the classification must remain ambiguous. ORFs for which an ORF-less orthologous location cannot be found cannot be defined as de novo or new, as we cannot exclude the possibility that they are ancient but fast evolving. The approach using sequence similarity alone can, at best, suggest that the new gene bears no resemblance to extant genes or horizontally transferred genes, thus implicating de novo origination by exclusion. If no attempt is made to reconstruct the ancestral state or if it is not practically possible to do so, these are classified as 'putatively de novo genes' and are not considered in this taxonomy. We propose a hierarchical classification of de novo genes based on whether or not there is newly inserted sequence in the locus and whether or not that sequence had been previously under natural selection: type Ia and type Ib are entirely derived from non-protein-coding sequence; type II contains a minority of sequence that was previously under selection (such as transposable elements or portions of a pre-existing gene), but that does not explain the function of the modern gene; and type III de novo genes are chimaeras of sequences previously under selection, but which contain some novel sequence not previously under selection for protein-coding function. Type I genes are the most clean-cut, whereas the gene histories for type II and type III are progressively more convoluted. Real world complexity probably means that type III genes will be contested in some instances. For example, jingwei (jgw) has not previously been considered as a de novo gene, but it is a new gene that includes previously intronic (that is, non-protein-coding) sequence, and classifying it as a type III de novo gene acknowledges this mixed history. CLLU1, chronic lymphocytic leukaemia upregulated 1; D. melanogaster, Drosophila melanogaster; ESRG, embryonic stem cell related; H. sapiens, Homo sapiens; PBOV1, prostate and breast cancer overexpressed 1; S. cerevisiae, Saccharomyces cerevisiae.

  2. Validation of novel genes.
    Figure 2: Validation of novel genes.

    There are significant challenges in verifying lineage-specific de novo genes owing to the unavailability of some tools and the uninformative nature of others. Well-established genes receive support from sequence similarity across many genomes and evolutionary patterns of selection, and a certain fraction of them will show a phenotype in a knockout or knockdown experiment. For most of these tests, species-specific genes are indistinguishable from spurious expression in the genome. Functional characterization through observation of knockdown or knockout phenotypes is one way to distinguish genuine novel genes from spurious expression. Note that the distinction between 'taxonomically restricted' and 'species-specific' need not be absolute in that the latter can become the former when more closely related genomes are added. In the lower panel, ticks indicate observed and crosses indicate not observed. NA, not available; ORF, open reading frame.

  3. Features of genome anatomy that alter the likelihood of novel gene origination.
    Figure 3: Features of genome anatomy that alter the likelihood of novel gene origination.

    a | A pre-existing gene (dark blue box) may facilitate the origin of a de novo gene (light blue box) through the re-use of the promoter, perhaps in a bidirectional conformation. b | A pre-existing gene may also contribute to novel gene origination through transcriptional read-through, which can occur in as many as 11% of cases. c | Start (ATG) and stop (TAA, TAG and TGA) codons are AT-rich and are thus less frequent in GC-rich regions of the genome. This means that the distance between any start and stop codon is longer in GC-rich regions of genome, resulting in longer random open reading frames (ORFs; light blue boxes). Conversely, although stop codons are common in GC-poor regions, so are start codons; thus, random ORFs will be short but so will the inter-ORF distances, resulting in high ORF density. d | Transposable elements (yellow boxes) can facilitate the origin of new genes by providing regulatory sequences (arrows) or by contributing to the ORF of the novel gene (light blue boxes). e | Mutation of a transcription factor (TF) may alter its DNA-binding specificity, thus activating expression at many previously unexpressed loci (light blue boxes) with or without affecting the expression of pre-existing genes (dark blue boxes).

Change history

Corrected online 27 July 2016
In Table 1 of the original version of this article the gene name NCYM was incorrectly written as NYCM. This has now been corrected. The editors apologize for this error.

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Affiliations

  1. The Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland.

    • Aoife McLysaght
  2. The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK.

    • Laurence D. Hurst

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The authors declare no competing interests.

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  • Aoife McLysaght

    Aoife McLysaght is a professor in genetics at the University of Dublin, Trinity College, Ireland, where she also obtained her Ph.D. Her research is in molecular evolution, using bioinformatics and computational biology approaches. Her principal research focus is the evolution of vertebrate genomes with respect to fundamental questions surrounding new genes, gene and genome duplication, and evolutionary constraints.

  • Laurence D. Hurst

    Laurence D. Hurst is Director of the Milner Centre for Evolution, Director of the Genetics and Evolution Teaching Project and a professor of evolutionary genetics at the University of Bath, UK. He received his B.A. from the University of Cambridge, UK, and his D.Phil. from the University of Oxford, UK. He is interested in fundamental problems concerning the evolution of genes, genomes and genetic systems.

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