New genes and functional innovation in mammals

Abstract

The birth of genes that encode new protein sequences is a major source of evolutionary innovation.However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions we have obtained a large collection of mammalian-specific 5 gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mamalian species, obtaining about 6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the 10 functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from non-coding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important 15 role in the emergence of new functional genes.

The relationship of mRNA with protein expression in CD8+T cells associates with gene class and gene characteristics

“…We next sought to identify which features in the mRNA could explain the discrepancy of mRNA and protein expression. High sequence conservation has been associated with high gene expression levels in mammals (Villanueva-Cañas et al, 2017). We therefore questioned whether this was also true for both mRNA and protein abundance in PMA-Ionomycin activated CD8 + T cells.…”

That is life: communicating RNA networks from viruses and cells in continuous interaction

“…Such noncoding RNAs most often derive from mobile genetic elements and are the major contributors to regulatory ncRNAs, which include endogenous retroviruses, their defective derivatives, and other persistent genetic parasites (not forgetting their degraded parts). [35][36][37][38][39][40] Another highly interesting interaction motif of RNAs is the RNA fragments that self-ligate into selfreplicating ribozymes, which spontaneously form cooperative networks. It was found that the threemembered RNA networks showed highly cooperative growth dynamics.…”

Many but not all lineage-specific genes can be explained by homology detection failure

“…For example, lineage-specific genes have been interpreted as "de novo genes" that have evolved from previously noncoding sequence [10,11], and as duplicated genes that diverged radically in evolving a new function [12]. Though different in detail, these proposals share the key assumption that a lack of detectable homologs indicates some kind of biological novelty: lineage-specific genes either have no evolutionary homologs or no longer perform the same function as their homologs outside the lineage [13][14][15][16]. We refer to these interpretations collectively as the "novelty hypothesis" of lineage-specific genes.…”