Podcast: Mapping childhood mortality, and evolving ‘de novo’ genes

Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses show that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last ~15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis.

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Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina

10.7287/peerj.preprints.3030 ◽

2017 ◽

Author(s):

William Blevins ◽

Mar Albà ◽

Lucas Carey

Keyword(s):

De Novo ◽

Ribosome Profiling ◽

Rna Seq ◽

De Novo Genes ◽

De Novo Gene ◽

Rich Media ◽

Conserved Genes ◽

Different Depths ◽

Yeast Phylogeny ◽

And Oxidative Stress

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology with other genes. Furthermore, de novo genes may not initially be under the same selective constraints as other genes. Dozens of de novo genes have recently been identified in many diverse species; however, the mechanisms leading to their appearance are not yet well understood. To study this phenomenon, we have performed deep RNA sequencing (RNA-seq) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. Furthermore, we performed ribosome profiling (Ribo-seq) experiments in both conditions with S. cerevisiae. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (unannotated), and many were identified as putative de novo genes; these candidates were then tested for signals of translation using our Ribo-seq data. We show that putative de novo genes have different properties relative to phylogenetically conserved genes. This comparative phylotranscriptomic analysis advances our understanding of de novo gene origins.

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De Novo Genes are “Frozen Accidents” which Escaped Rapid Turnover of Pervasively Transcribed ORFs

10.1101/166827 ◽

2017 ◽

Author(s):

Jonathan Schmitz ◽

Kristian Ullrich ◽

Erich Bornberg-Bauer

Keyword(s):

De Novo ◽

Nucleotide Composition ◽

Open Reading Frames ◽

Evolutionary Time ◽

High Coverage ◽

De Novo Genes ◽

Protein Properties ◽

Genetic Mechanisms ◽

Reading Frames ◽

Gene Age

AbstractA recent surge of studies suggested that many novel genes arise de novo from previously non-coding DNA and not by duplication. However, since most studies concentrated on longer evolutionary time scales and rarely considered protein structural properties, it remains unclear how these properties are shaped by evolution, depend on genetic mechanisms and influence gene survival. Here we compare open reading frames (ORFs) from high coverage transcriptomes from mouse and another four mammals covering 160 million years of evolution. We find that novel ORFs pervasively emerge from intergenic and intronic regions but are rapidly lost again while relatively fewer arise from duplications but are retained over much longer times. Surprisingly, disorder and other protein properties of young ORFs do not change with gene age. Only length and nucleotide composition change, probably to avoid aggregation. Thus de novo genes resemble frozen accidents of randomly emerged ORFs which survived initial purging, likely because they are functional.

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