Genes & genetic systems最新文献

Roles of endogenous retrovirus- and other LTR retrotransposon-derived proteins and peptides in neurological disorders, oncogenesis, and host defense. 内源性逆转录病毒和其他LTR逆转录转座子衍生蛋白和肽在神经系统疾病、肿瘤发生和宿主防御中的作用。

IF 0.9 4区生物学

Genes & genetic systems Pub Date : 2026-10-15 DOI: 10.1266/ggs.26-00069

Noi Saitoh, Ryo Yanagiya, Yi Cong, So Nakagawa

引用次数: 0

Co-option of retroviral genes: diversity and evolution in vertebrates. 逆转录病毒基因的共同选择：脊椎动物的多样性和进化。

IF 0.9 4区生物学

Genes & genetic systems Pub Date : 2026-09-02 DOI: 10.1266/ggs.26-00068

Koichi Kitao

{"title":"Co-option of retroviral genes: diversity and evolution in vertebrates.","authors":"Koichi Kitao","doi":"10.1266/ggs.26-00068","DOIUrl":"https://doi.org/10.1266/ggs.26-00068","url":null,"abstract":"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.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Regulation of Fhl1 function through interactions with Hmo1 and Fpr1 at ribosomal protein gene promoters in Saccharomyces cerevisiae. 酿酒酵母核糖体蛋白基因启动子上Hmo1和Fpr1相互作用对Fhl1功能的调控

IF 0.9 4区生物学

Genes & genetic systems Pub Date : 2026-08-13 Epub Date: 2026-06-17 DOI: 10.1266/ggs.26-00060

Naoki Shimamura, Koji Kasahara

{"title":"Regulation of Fhl1 function through interactions with Hmo1 and Fpr1 at ribosomal protein gene promoters in Saccharomyces cerevisiae.","authors":"Naoki Shimamura, Koji Kasahara","doi":"10.1266/ggs.26-00060","DOIUrl":"10.1266/ggs.26-00060","url":null,"abstract":"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.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148270563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The L1-type adhesion molecule Neuroglian controls glial development and optic lobe morphogenesis in Drosophila. l1型粘附分子，神经胶质，控制果蝇胶质细胞发育和视叶形态发生。

IF 0.9 4区生物学

Genes & genetic systems Pub Date : 2026-07-25 Epub Date: 2026-05-26 DOI: 10.1266/ggs.26-00023

Yufan Jin, Takumi Morita, Yuichi Ishiwata, Hiroki Takechi, Tomoyuki Yoshida, Tatsuya Niwa, Satoko Hakeda-Suzuki, Jiro Osaka, Takashi Suzuki

{"title":"The L1-type adhesion molecule Neuroglian controls glial development and optic lobe morphogenesis in Drosophila.","authors":"Yufan Jin, Takumi Morita, Yuichi Ishiwata, Hiroki Takechi, Tomoyuki Yoshida, Tatsuya Niwa, Satoko Hakeda-Suzuki, Jiro Osaka, Takashi Suzuki","doi":"10.1266/ggs.26-00023","DOIUrl":"10.1266/ggs.26-00023","url":null,"abstract":"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.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148042051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SSR marker development for Japanagromyza tokunagai (Agromyzidae, Diptera) using genome sequences obtained by nanopore sequencing. 利用纳米孔测序技术开发双翅目稻蛾（Japanagromyza tokunagai）的SSR标记。

IF 1.2 4区生物学

Genes & genetic systems Pub Date : 2026-06-13 Epub Date: 2026-04-08 DOI: 10.1266/ggs.25-00074

Yumi Yamashita, Leiko Mizusawa, Yuki Ogura-Tsujita, Shingo Kaneko

引用次数: 0

Phylogenetic and population genomic analysis of foxtail millet (Setaria italica) landraces via ddRAD-seq, with emphasis on Japanese germplasm. 利用ddRAD-seq技术分析地方小谷子的系统发育和群体基因组，以日本品种为重点。

IF 1.2 4区生物学

Genes & genetic systems Pub Date : 2026-06-06 Epub Date: 2026-04-10 DOI: 10.1266/ggs.26-00012

Kenji Fukunaga, Akira Abe, Keisuke Tanaka, Masaya Tsuji, Makoto Kawase

{"title":"Phylogenetic and population genomic analysis of foxtail millet (Setaria italica) landraces via ddRAD-seq, with emphasis on Japanese germplasm.","authors":"Kenji Fukunaga, Akira Abe, Keisuke Tanaka, Masaya Tsuji, Makoto Kawase","doi":"10.1266/ggs.26-00012","DOIUrl":"10.1266/ggs.26-00012","url":null,"abstract":"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.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":""},"PeriodicalIF":1.2,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147672574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The 2^nd Asian Genetics Consortium Conference 2025 (AGCC 2025) -Genetics in Asia: Heredity, Diversity, Discovery, and Beyond. 第二届亚洲遗传联盟会议2025 （AGCC 2025）。

IF 0.9 4区生物学

Genes & genetic systems Pub Date : 2026-06-05 Epub Date: 2026-04-15 DOI: 10.1266/ggs.26-00026

So Nakagawa, Hiroshi Iwasaki, Takehiko Kobayashi, Takuji Kakutani

引用次数: 0

KLF5 modulates NTSR1 to facilitate fatty acid oxidation and repress anoikis in gastric cancer. KLF5调节NTSR1促进脂肪酸氧化，抑制胃癌的癌变。

IF 0.9 4区生物学

Genes & genetic systems Pub Date : 2026-05-09 Epub Date: 2026-02-17 DOI: 10.1266/ggs.24-00196

Piyao Gao, Cheng Zhang, Shibiao Zhong, Jianbao Wei, Hui Ma

{"title":"KLF5 modulates NTSR1 to facilitate fatty acid oxidation and repress anoikis in gastric cancer.","authors":"Piyao Gao, Cheng Zhang, Shibiao Zhong, Jianbao Wei, Hui Ma","doi":"10.1266/ggs.24-00196","DOIUrl":"10.1266/ggs.24-00196","url":null,"abstract":"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.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146219419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Universality and diversity of gene expression patterns in response to cold acclimation in Drosophila albomicans. 白果蝇冷驯化基因表达模式的普遍性和多样性。

IF 0.9 4区生物学

Genes & genetic systems Pub Date : 2026-05-01 Epub Date: 2026-02-11 DOI: 10.1266/ggs.25-00085

Shikha Singh, Tomohiko Kimura, Koichiro Tamura

{"title":"Universality and diversity of gene expression patterns in response to cold acclimation in Drosophila albomicans.","authors":"Shikha Singh, Tomohiko Kimura, Koichiro Tamura","doi":"10.1266/ggs.25-00085","DOIUrl":"10.1266/ggs.25-00085","url":null,"abstract":"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.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146164965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure and evolution of the sequence-specific anti-silencing factor VANC21 and its target DNA. 序列特异性抗沉默因子VANC21及其靶DNA的结构与进化

IF 1.2 4区生物学

Genes & genetic systems Pub Date : 2026-02-03 Epub Date: 2025-11-19 DOI: 10.1266/ggs.25-00096

Yusaku Tanaka, Akihisa Osakabe, Wataru Shihoya, Hisato Hirano, Yuzuru Itoh, Tetsuji Kakutani, Osamu Nureki

{"title":"Structure and evolution of the sequence-specific anti-silencing factor VANC21 and its target DNA.","authors":"Yusaku Tanaka, Akihisa Osakabe, Wataru Shihoya, Hisato Hirano, Yuzuru Itoh, Tetsuji Kakutani, Osamu Nureki","doi":"10.1266/ggs.25-00096","DOIUrl":"10.1266/ggs.25-00096","url":null,"abstract":"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.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":""},"PeriodicalIF":1.2,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145556688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0