Emergence of a New Gene from an Intergenic Region

Abstract

It is generally assumed that new genes would arise by gene duplication mechanisms, because the signals for regulation and transcript processing would be unlikely to evolve in parallel with a new gene function. We have identified here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5-3.5 million years in a large intergenic region. The region is present in many mammals, including humans, allowing us to exclude the involvement of gene duplication, transposable elements, or other genome rearrangements, which are typically found for other cases of newly evolved genes. The gene has three exons, shows alternative splicing, and is specifically expressed in postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus and its emergence correlates with indel mutations in the 5' regulatory region of the transcript. A recent selective sweep is associated with the transcript region in M. m. musculus populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and reduced testis weight. Our results show that cryptic signals for transcript regulation and processing exist in intergenic regions and can become the basis for the evolution of a new functional gene.

Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition

“…How these recently originated genes became integrated into pathways and how they conferred a male-related fitness advantage can be deciphered unambiguously only by performing molecular and functional analyses in which these new functions are impaired and the phenotypic consequences monitored. Although still scarce, this type of study has confirmed the contribution of newly evolved genes to sperm production (12), sperm function upon fertilization (13), sperm individualization and motility (14,15), and male courtship (16). Among these case studies, only one (16) involves a species-specific gene.…”

Critical roles of long noncoding RNAs in Drosophila spermatogenesis

“…However, it remains unclear whether lncRNAs are truly involved in male reproduction in vivo. Three mouse lncRNAs are involved in spermatogenesis in vitro Ni et al 2011;Arun et al 2012), but the aforementioned Pldi RNA represents the only case in which functional significance in spermatogenesis has been demonstrated in lncRNA knockout models (Heinen et al 2009). Thus, we attempted to survey the functional roles of lncRNAs in spermatogenesis using our optimized CRISPR system.…”

“…Moreover, lncRNAs participate with protein-coding genes in evolutionarily conserved coexpression networks during spermatogenesis (Necsulea et al 2014), the process by which male germline stem cells (GSCs) divide and differentiate into mature sperm in sexual organisms. To date, however, the functional significance of lncRNAs in spermatogenesis is unknown, with a few exceptions such as polymorphic derived intron-containing (Pldi) RNA (Heinen et al 2009). To gain a comprehensive picture of lncRNA functionality in spermatogenesis, it is necessary to develop an efficient and large-scale gene knockout method for investigating the functions of lncRNAs in intact organisms.…”

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

“…Can novel genes arise de novo from previously gene-free neutrally evolving genome regions? Despite some false positives (Monte et al 1997;Kriegs et al 2005), recruitment of entire protein-coding genes out of neutrally evolving sequences does occur (Long et al 2003Heinen et al 2009;Kaessmann 2010;Carvunis et al 2012;Murphy and McLysaght 2012;Neme and Tautz 2013). Recently, it has been emphasized that many long non-protein-coding RNAs originated from TEs (Kapusta et al 2013).…”