Endogenous retroviruses (ERVs) are remnants of retroviral sequences that integrated into the host germline genome and are inherited across generations. Occasionally, the protein-coding genes within ERVs have been co-opted as host genes and contribute to diverse biological processes. In early studies, the identified ERV-derived genes remained taxonomically restricted to model organisms. Recently, however, the increasing availability of vertebrate genome assemblies has expanded the known repertoire of ERV-derived genes across diverse lineages. Here, I review the current knowledge of ERV-derived genes and how the era of comparative genomics is reshaping our understanding of the vertebrate ERV-derived genes. I first describe the processes of ERV endogenization, genomic expansion, and co-option. Then, I summarize the known functions of ERV-derived genes in vertebrates and the methodology of comparative genomic approaches to discover ERV-derived genes. I further discuss evolutionary models of ERV-derived genes, which will become increasingly important for understanding the broad pattern of their evolution. This review also provides a catalog of ERV-derived genes, including recently identified genes of unknown function. By integrating findings from recent comparative genomic studies, this review provides an updated view of how ERV-derived genes have contributed to vertebrate evolution.
In budding yeast Saccharomyces cerevisiae, Ifh1 (interacts with fork head 1) is a transcriptional co-activator that is essential for growth and is recruited to ribosomal protein gene (RPG) promoters through interaction with the forkhead-associated (FHA) domain of fork head-like 1 (Fhl1). However, the lethality of ifh1Δ cells is rescued by deletion of FHL1 or its FHA domain, suggesting that the essential function of Ifh1 is suppressing FHA domain-mediated growth inhibition. In our recent study, we found that deletion of previously uncharacterized C-terminal regions, as well as the FHA domain, of Fhl1 rescues the lethality of ifh1Δ cells. We report here that chromatin immunoprecipitation analysis of Fhl1 deletion mutants showed that deletion of the 754-844 aa region significantly decreased binding to category 1 RPG promoters, which are enriched for high mobility group 1 (Hmo1) binding, whereas deletion of the 572-662 aa region markedly reduced binding to all RPG promoters examined. These results suggest that reduced Fhl1 binding to RPG promoters enables growth of the ifh1Δ cells. Because Fhl1 binding is regulated by Hmo1 and/or FK506-sensitive proline rotamase 1 (Fpr1), we examined the effect of HMO1 deletion and found that the hmo1Δifh1Δ double mutant became viable. Yeast two-hybrid analysis revealed that the 754-844 aa region of Fhl1 interacts with Hmo1, particularly its box B domain, suggesting that this interaction contributes to the recruitment of Fhl1 to category 1 RPG promoters. Furthermore, we observed a weak interaction between Fpr1 and the 540-662 aa region of Fhl1. Genetic analysis showed that fhl1Δfpr1Δ double mutants exhibited much more severe growth defects than either single mutant, indicating that both proteins cooperatively play important roles in yeast growth, although the underlying mechanism remains unclear. Collectively, these results suggest that Hmo1 and Fpr1 regulate Fhl1 function, which exerts both negative and positive effects on yeast growth.
Glial development is essential for establishing the architecture and connectivity of the Drosophila visual system. However, the molecular programs that coordinate glial proliferation, differentiation, migration and wrapping during optic lobe maturation remain incompletely defined. Here, we identify the homophilic L1-type adhesion molecule Neuroglian (Nrg) as a key regulator of glial development and tissue-scale remodeling in the developing optic lobe. Glia-specific depletion of Nrg disrupts the characteristic lamina-medulla rotation during pupation, causes fragmentation and loss of continuity of wrapping-glial membranes, and significantly reduces the number of glial cells, accompanied by increased glial apoptosis and only marginal changes in glial proliferation after normalization to total glial cell number, revealing a broad requirement for Nrg across multiple stages of glial development. Subtype-specific knockdown demonstrates that giant chiasm glia and cortex glia are important for Nrg-mediated glial development, migration and differentiation as well as axon wrapping and proper optic lobe geometry. Finally, using isoform-specific endogenous tagging, we show that Nrg167, rather than Nrg180, is the predominant glial isoform from the third-instar larval stage through adulthood. Together, our findings establish an isoform-specific, glia-intrinsic role for Nrg in coupling cellular morphogenesis to organ-level visual system assembly and highlight cell adhesion molecules as a core determinant of neural tissue architecture.
We clarified the phylogeny and population structure of foxtail millet (Setaria italica (L.) P. Beauv.) landraces using ddRAD-seq, which also enabled us to focus in detail on Japanese landraces. The results were compared with those of previous phylogenetic studies based on transposon display and genotyping of individual genes involved in domestication and diversification under natural and artificial selection. Foxtail millet landraces were found to cluster into distinct geographical groups. The comparison revealed that certain genes, such as Heading date 1, began diverging soon after domestication. In contrast, genes such as Pseudo-response regulator 37 appeared to have differentiated before geographic divergence, likely in response to environmental adaptation. However, genes such as Waxy loci diversified after geographic separation under human selection. Implication of introgression between geographically distant groups was also observed, for example, between French and East Asian landraces. In Japan, two distinct landrace groups were identified: one closely related to Korean landraces and the other showing genetic similarity to accessions from Taiwan and the Batan Islands of the Philippines. The latter group is predominantly distributed in the Nansei Islands (Okinawa Prefecture), indicating multiple introductions and complex dispersal histories of foxtail millet in Japan.
