Origins of de novo genes in human and chimpanzee

TL;DR

This study investigates the origins of de novo genes in humans and chimpanzees by sequencing transcriptomes, revealing numerous new transcripts, some with coding potential, and providing evidence for their possible functional roles in evolution.

Contribution

It offers a comprehensive analysis of de novo gene emergence, identifying regulatory features and translation evidence, advancing understanding of how new genes evolve from non-coding regions.

Findings

Over five thousand new transcripts identified in human and chimpanzee.

New transcripts are associated with gain of regulatory motifs and U1 snRNP sites.

Several de novo genes show translation evidence and signs of purifying selection.

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 do not contain any gene or gene copy. 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 transcriptional multiexonic events in human and/or chimpanzee that are not observed in the rest of species. By 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. We also find that the coding potential of the new genes is higher than expected by chance, consistent with the presence of protein-coding genes in the dataset. Using available human tissue proteomics and ribosome profiling data we identify several de novo genes with translation evidence. These genes show significant purifying selection signatures, indicating that they are probably functional. Taken together, the data supports a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.