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.
Japanagromyza tokunagai Sasakawa 1953 (Agromyzidae, Diptera) disrupts seed reproduction of orchids by feeding on orchid fruit. This species has been feeding on orchid fruits in Japan for more than 100 years, but the recent increase in damage may be due to the spread of particularly harmful populations. In this study, we used nanopore sequencing to establish microsatellite markers for J. tokunagai to infer the cause of this fly's spreading history based on population genetic analysis of historical specimens and current samples. Analysis of three populations showed that all 15 loci of the microsatellite markers that we established were polymorphic and the number of alleles ranged between 3 and 13. The markers developed in this study can be used to reveal current and past population genetic diversity and gene flow, contributing to our understanding of the population history of this parasitic fly. Further research using these markers will provide a foundation for developing control methods for J. tokunagai and support the conservation of rare orchid plants.
Neurotensin receptor 1 (NTSR1) is linked with poor prognosis in many tumors, including gastric cancer (GC). However, the exact mechanism by which NTSR1 affects GC anoikis in GC is uncharted. Therefore, we aimed to elucidate the specific mechanism by which NTSR1 participates in GC anoikis. We used qRT-PCR (quantitative reverse transcription polymerase chain reaction) to assess the levels of NTSR1 and its upstream transcription factor KLF5 (a key member of the Kruppel-like factor family) in GC tissues, and bioinformatics to analyze the signaling pathways in which NTSR1 participated. A CCK-8 kit was applied to detect the viability of GC cells under different treatments. Dual luciferase and chromatin immunoprecipitation experiments verified the binding relationship between KLF5 and NTSR1. The rate of fatty acid oxidation (FAO) was analyzed using a cell metabolism meter, and FAO-related protein expression was detected using western blot (WB). Anoikis of cells in each treatment group was detected using flow cytometry, an anoikis apoptosis kit and WB. Knocking down NTSR1 repressed the viability of GC cells, and elevated the anoikis rate and the expression of cleaved PARP and cleaved caspase-3 in GC cells. Moreover, high expression of NTSR1 upregulated the expression of CPT1 protein in FAO and increased FAO levels, thereby suppressing the occurrence of anoikis in GC cells. Addition of the FAO inhibitor etomoxir reversed the above trends. Additionally, KLF5 was highly expressed in GC. Finally, KLF5 knockdown was found to overcome the repression of the FAO pathway and to facilitate anoikis in GC cells that were overexpressing NTSR1. In summary, KLF5 affects anoikis in GC cells by targeting NTSR1 to modulate the FAO pathway. Therefore, blocking the FAO pathway regulated by the KLF5/NTSR1 axis may become a new strategy for the treatment of GC.
Cold acclimation, defined as gradual habituation to low temperatures by exposure to moderately cold temperatures for several days, is known to enhance an organism's cold tolerance and facilitate its adaptation to seasonal temperature changes in temperate regions. The present study focuses on the evolution of the cold acclimation response in Drosophila albomicans, which rapidly expanded its distribution from tropical Southeast Asia to the Japanese main islands in the mid-1980s. This research aims to elucidate the genetic mechanisms underlying cold acclimation through gene expression changes. The gene expression changes due to cold acclimation were compared among five strains with different genetic backgrounds to identify the genes involved in these processes. High-throughput mRNA sequencing was employed to identify differentially expressed genes (DEGs) in strains from China, Taiwan and Japan under cold acclimation and control conditions. The results suggest that the actin genes play a critical role in cellular functions at low temperatures. A reduction in the expression of mElo is likely to result in decreased levels of C18 fatty acids, thereby enhancing cellular cold tolerance. Furthermore, this study highlights the universality and diversity of gene expression changes in response to cold acclimation. While many DEGs shared by all five strains were genes involved in metabolic pathways, many strain-specific DEGs were genes involved in gene regulation. This suggests that genes with critical roles in fundamental cellular and physiological processes are subject to evolutionary constraints, whereas those involved in regulatory functions or responding to local environmental conditions undergo rapid evolution to exhibit significant variability. These results provide insight into the genetic mechanisms of environmental adaptation and population expansion in nature.
VANDAL family DNA transposons are prevalent in Arabidopsis and related plants. A notable feature of VANDALs is that they can overcome epigenetic silencing from the host, using a VANC protein encoded in each VANDAL member: VANC21 protein encoded in VANDAL21 specifically accumulates on its target DNA motifs that are concentrated in the non-coding regions of this TE and induces loss of DNA methylation, transcriptional derepression, and mobilization of the element. In this study, to elucidate the mechanism of how VANC subtypes have diverged to bind specifically to their own target motifs in their cognate VANDAL subfamilies, we determined the crystal structure of VANC21 in complex with its target DNA at 2.0 Å resolution. The VANC structure adopts a globular novel fold with a Zn ion coordinated at the DNA-binding site. Interestingly, most DNA-interacting VANC residues are located in the loops but not in the conserved regions among VANC subtypes. This observation suggests that the high variability of DNA-interacting regions of VANC proteins brought about the co-evolution of VANCs and their target sequences. This rapid differentiation by co-evolution enabled VANDAL family TEs to proliferate while avoiding deleterious effects on host fitness. Therefore, our findings help to understand the adaptive evolutionary strategy for the survival of parasitic sequences.
Primula tibetica is an insect-pollinated, herbaceous, perennial plant belonging to the section Aleuritia (Primulaceae). The species exhibits the typical characteristics of heterostyly, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs. Furthermore, significant variation occurs in floral morphology, categorised as homostyly, a phenomenon commonly associated with elevated selfing rates. Utilising next-generation sequencing, 25 microsatellite markers for P. tibetica were developed, with the objective of facilitating future investigations into the population genetics and mating patterns of the species. These markers were characterised by measuring polymorphism and genetic diversity in a sample of 36 individuals from three natural populations. The markers displayed relatively high polymorphism, with the number of observed alleles per locus ranging from two to 15 (mean = 7.26). The observed and expected heterozygosities ranged from 0.056 to 0.917 and 0.105 to 0.825, respectively. Furthermore, nineteen of these loci were also successfully amplified in P. pulchella. These microsatellite markers should serve as effective tools for investigating patterns of population genetic diversity and elucidating the evolutionary relationship between distyly and homostyly in P. tibetica.
Ancient dispersal events from the Korean Peninsula to the Japanese main islands of Honshu, Shikoku and Kyushu (HSK), and from the Eurasian continent to Hokkaido via Sakhalin, have played a critical role in shaping the mammalian diversity of the Japanese archipelago. However, the timing and dynamics of these events remain incompletely understood across different taxa. In addition, the 100,000-year climatic cycles of glacial and interglacial periods during the Middle and Late Quaternary likely influenced intraspecific genetic diversity, although the mechanisms driving these changes remain unclear. In this study, we analyzed mitochondrial cytochrome b gene sequences from Japanese shrews (Sorex and Crocidura) and other small mammals from HSK and Hokkaido. Using an evolutionary rate of 0.029 substitutions/site/million years, we inferred that ancestral lineages of HSK species diverged during critical periods in the early Quaternary, such as around 2.4 and 1.7 million years ago (Ma), potentially in response to major climatic transitions. Notably, dispersal events of the Laxmann's shrew (S. caecutiens) and dark red-backed vole (Myodes rex) into Hokkaido around 1.7 Ma were also suggested. Regarding intraspecific mitochondrial DNA (mtDNA) lineages, species with broad distributions in HSK typically exhibit a north-south structure, characterized by two major lineages, as well as additional ancient lineages in surrounding offshore islands. Comparative analysis revealed that divergence among these lineages occurred at approximate intervals of 100,000 years. Our results indicate that the mtDNA genetic structure of HSK small mammals reflects geographic substructures shaped by climate-driven dispersal. Regions that facilitated rapid expansion during favorable climatic periods likely acted as centers of dispersal, from which haplotypes spread toward peripheral areas. As haplotypes radiated outward from these core regions, distinct mtDNA lineages became established across different geographic zones, giving rise to the spatial distribution patterns observed today.
In most eubacteria the initiator protein DnaA triggers chromosomal replication by forming an initiation complex at the origin of replication and also functions as a transcriptional regulator, coordinating gene expression with cell cycle progression. While genes regulated by DnaA are relatively well characterized in exponentially growing cells, its role in gene regulation during stationary phase remains insufficiently explored. Here, using the aquatic bacterium Caulobacter crescentus as a model, we show that C. crescentus DnaA (ccDnaA) acts as a repressor of the previously uncharacterized CCNA_00139 gene, which encodes a YifB family Mg chelatase-like AAA ATPase family protein of unknown function. Biochemical analyses reveal that ccDnaA forms multimers at this site, which may interfere with RNA polymerase access to the promoter by occupying overlapping binding sequences. Consistent with these findings, in exponentially growing C. crescentus cells the CCNA_00139 promoter is repressed in a ccDnaA-dependent manner. Notably, when cells enter stationary phase, CCNA_00139 promoter activity increases in parallel with ccDnaA clearance, supporting the idea that ccDnaA-mediated repression is relieved during this phase transition. Despite its regulated expression, deletion of CCNA_00139 did not result in any detectable growth, replication or DNA damage sensitivity phenotypes under the tested laboratory conditions, suggesting a possible role under specific environmental conditions. Given that this phase-dependent transcriptional switch may, in principle, apply to other uncharacterized ccDnaA-repressed genes, we infer that CCNA_00139, along with other such genes, form a regulatory network that supports quorum sensing or adaptation to growth phase transitions. We believe that these findings offer new insight into the potential role of bacterial DnaA in regulating gene expression in dormant or non-replicating cells across diverse bacterial species.
In our study, we aimed to identify new mutants resulting from ONSEN transposition in Arabidopsis thaliana by subjecting nrpd1 mutants to heat stress. We isolated a mutant with a significantly elongated hypocotyl, named "Long hypocotyl in ONSEN inserted line 1" (HYO1). This phenotype was heritable, with progeny consistently displaying longer hypocotyls than the wild type. Genetic analysis revealed that this trait was due to a single recessive mutation. Further mapping and sequencing identified the insertion of ONSEN in the HY2 gene, a crucial regulator of hypocotyl elongation. The insertion disrupted HY2 transcription, as confirmed by quantitative PCR, leading to the observed phenotype. To assess the influence of the nrpd1 background, we generated lines backcrossed twice to wild-type Col-0, and the results were consistent with those observed in the original mutant lines. Furthermore, we examined the effect of HY2 and HYO1 mutations on flowering time by analyzing the expression levels of FT. The hyo1 mutant exhibited earlier flowering compared to both the wild type and nrpd1 mutants, with increased FT expression levels. This research underscores the significant impact of ONSEN transposition on gene function and phenotypic variation in Arabidopsis thaliana, providing new insights into the mutagenic potential of transposons and their role in shaping plant traits.
The mammalian sex-determining gene SRY is highly conserved across species, with only a few exceptions. The Japanese rodent genus Tokudaia is known for its unique sex chromosome evolution. The Okinawa spiny rat Tokudaia muenninki (TMU) acquired neo-sex chromosomes with multiple Sry copies by sex chromosome-autosome fusions. All SRY copies in TMU have a substitution from alanine to serine at position 21 in the high-mobility group (HMG) box, a critical DNA-binding domain, suggesting that they are nonfunctional. However, the sex determination system in TMU remains unclear, in part because the species is endangered and it is therefore extremely difficult to obtain experimental samples. In this study, we performed in silico and in vitro analyses to investigate the molecular properties and function of SRY using recently obtained whole genome sequence and RNA-seq data. A comparison of SRY sequences from 225 species showed that TMU is the only species with a substitution at the 21st position. This result highlights the rarity and specificity of this substitution. Structural predictions, DNA docking simulations, electrophoretic mobility shift assays, and fluorescence anisotropy showed that although the affinity was slightly lower than that of the mouse homolog, DNA-binding ability was retained. However, Sry expression was not detected in the testis, liver, and brain in adult TMU. The complete absence of Sry expression in the adult tissues, despite an intact sequence, strongly indicates a loss of regulatory function. These findings provide insight into the unique evolution of Sry gene in this species.
Maintenance DNA methylation is essential for the stable inheritance of epigenetic information in vertebrates. While DNMT1 has long been recognized as the principal maintenance methyltransferase, recent studies have shown that its activity critically depends on ubiquitin signaling. Specifically, the E3 ligase UHRF1 enables DNMT1 recruitment and activation at hemimethylated sites through dual monoubiquitylation of both replication-associated and histone substrates. These insights have revised classical models of maintenance methylation and revealed new layers of regulation involving chromatin context, histone modifications and nucleosome remodeling. In this review, we summarize the current understanding of the molecular mechanisms underlying DNMT1-mediated maintenance methylation, with a particular focus on ubiquitin-dependent pathways and their interplay with chromatin architecture.
RNA sequencing analysis was performed to develop 16 novel expressed sequence tag-simple sequence repeat (EST-SSR) markers to evaluate genetic variation in the near-threatened halophyte Artemisia fukudo Makino, which inhabits riversides and tidal muds affected by brackish water at high tide. In the four populations examined, the total number of alleles at each locus ranged from two to 13, with an average of 4.3. The observed and expected heterozygosity ranged from 0.05 to 0.64 and 0.06 to 0.72, respectively. These newly developed EST-SSR markers will support the understanding of the population genetic structure of A. fukudo and contribute to the conservation of this species.
DNA methylation is essential for transcriptional regulation and the maintenance of chromosome stability, and its precise inheritance upon DNA replication is indispensable for cellular homeostasis. The DNMT1/UHRF1 complex is critical in copying DNA methylation with accessory proteins, including CDCA7 and HELLS. The DNMT1/UHRF1 complex is also crucial for maintaining DNA methylation at imprinting control regions during preimplantation development against genome-wide DNA demethylation, an essential process for early embryos to acquire totipotency. Pathogenic variants in the genes involved in the mechanism of DNA methylation maintenance result in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, multilocus imprinting disturbance (MLID), autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCADN), neuropathy, hereditary sensory, type 1E (HSN1E), Kleefstra syndrome 1 (KLEFS1) and immunodeficiency 96 (IMD96). This review discusses recent progress in understanding the molecular pathogenesis of these diseases, with a particular focus on ICF syndrome and MLID.
