Genes & genetic systems最新文献

{"title":"Multifaceted Roles of Transposons in Mammalian Evolution and the Future of Transposon Research.","authors":"Kei Fukuda","doi":"10.1266/ggs.98.287","DOIUrl":"10.1266/ggs.98.287","url":null,"abstract":"","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"98 6","pages":"287"},"PeriodicalIF":1.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722282","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}

{"title":"Mechanisms and impacts of genomic changes that are mediated by repetitive sequences in eukaryotes.","authors":"Mariko Sasaki","doi":"10.1266/ggs.98.101","DOIUrl":"10.1266/ggs.98.101","url":null,"abstract":"","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"98 3","pages":"101"},"PeriodicalIF":1.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41173103","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}

{"title":"GGS Prize 2023.","authors":"","doi":"10.1266/ggs.98.207","DOIUrl":"10.1266/ggs.98.207","url":null,"abstract":"","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"98 5","pages":"207-208"},"PeriodicalIF":1.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138290777","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}

{"title":"How to establish a mutually beneficial relationship between a transposon and its host: lessons from Tam3 in Antirrhinum.","authors":"Shasha Wang,&nbsp;Yohei Koide,&nbsp;Yuji Kishima","doi":"10.1266/ggs.22-00063","DOIUrl":"https://doi.org/10.1266/ggs.22-00063","url":null,"abstract":"<p><p>The transposon Tam3 of Antirrhinum (snapdragon) has acquired properties that distinguish it from other transposons. Mobile DNA, commonly referred to as a transposable element or transposon, is considered to be synonymous with a selfish factor. That is, a transposable element increases in copy number and moves copies of itself independently of the survival of the host organism. Therefore, the host collectively regulates the transposition activities of most transposable elements in its genome by epigenetic means. However, our analyses of the structure and behavior of Tam3, as shown by the following five results, provide evidence that it does not behave in a selfish manner in relation to the host. 1) Active transposable elements normally increase the abundance of their non-autonomous elements, whereas Tam3 is known to have no non-autonomous elements, and a limited number of around 10 copies of autonomous elements present in the genome have been isolated as active copies. 2) Tam3 does not transpose at 25 ℃, which is the optimal growth temperature for Antirrhinum. Transposition of Tam3 occurs only at low temperatures of about 15 ℃, which is stressful for Antirrhinum. 3) Few strains of Antirrhinum have been found to contain genes that specifically suppress Tam3 transposition. 4) Most of the Tam3 insertions found in Antirrhinum genes do not affect the host genome, and the expression of these host genes is not completely suppressed. 5) Transcription and translation of the Tam3 transposase gene are not epigenetically regulated by the host. These five experimental results constitute evidence that Tam3 retains features that are dissimilar to those of many other transposons and that it does not behave in a selfish manner that is detrimental to the survival of the host. In this review, we consider what kinds of behavior are required if transposons are to establish a mutually beneficial relationship with their hosts, with reference to Tam3.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"97 4","pages":"177-184"},"PeriodicalIF":1.1,"publicationDate":"2022-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10373928","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}

{"title":"Stress-responsive retrotransposable elements in conifers.","authors":"Tokuko Ujino-Ihara","doi":"10.1266/ggs.22-00042","DOIUrl":"https://doi.org/10.1266/ggs.22-00042","url":null,"abstract":"<p><p>Conifers are important in many forest ecosystems. They have a long generation time and are immobile; therefore, they require considerable plasticity to adapt to environmental stresses. Moreover, conifers have a large genome, a high proportion of which is occupied by repetitive elements. Retrotransposons are the most highly represented repetitive elements in conifers whose whole-genome sequences have been examined. These retrotransposons are usually silenced, to maintain genome integrity; however, some are activated by environmental stress. The insertion of retrotransposons into genic regions is associated with phenotypic and genetic diversity. The large number and high diversity of retrotransposons in conifer genomes suggest that they play a role in adaptation to the environment. In this review, progress in research on the roles of retrotransposons in the stress responses of conifers is reviewed, and potential future work is discussed.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"97 4","pages":"185-191"},"PeriodicalIF":1.1,"publicationDate":"2022-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10733645","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}

{"title":"Time series clustering analysis of genes during osteogenic differentiation of human mesenchymal stem cells.","authors":"Yaqiong Li,&nbsp;Jun Wang","doi":"10.1266/ggs.22-00068","DOIUrl":"https://doi.org/10.1266/ggs.22-00068","url":null,"abstract":"<p><p>To investigate the gene expression pattern and related biological changes during osteogenic differentiation of human mesenchymal stem cells (hMSCs), we downloaded expression data for four uninduced hMSC samples, and 12 osteogenic induction samples at day 2, 8, 12 or 25, in the GSE37558 dataset. Differentially expressed genes (DEGs) between groups were screened, followed by short time-series expression miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA). Osteogenic differentiation-related genes were extracted from the GeneCards database. Next, functional enrichment was performed, and protein-protein interaction (PPI) and lncRNA-miRNA-mRNA networks were constructed. Compared to uninduced hMSC samples, 163, 341, 447 and 537 DEGs were found in osteogenic induction samples at day 2, 8, 12 and 25, respectively, showing a sustainably increased trend. From STEM, WGCNA and the GeneCards database, a total of 107 key genes associated with osteogenic differentiation were screened; these genes were enriched in biological processes, such as ossification, ECM-receptor interaction, vasculature development, cartilage development and bone mineralization, as well as the Wnt signaling pathway and the chemokine signaling pathway. The PPI network identified four hub genes, STAT5A, TWIST1, FOXO1 and LEP. The lncRNA-miRNA-mRNA network revealed regulatory axes for STAT5A, FOXO1 and LEP. Three and two regulatory axes were found for STAT5A and LEP, respectively. Multiple regulatory axes for FOXO1 were found, such as MIR155HG-miR-223-FOXO1. This study identifies candidate key targets that may play important roles in regulating osteogenic differentiation of hMSCs, and provides novel information to further investigate the molecular regulation mechanism. More experiments are required to evaluate the effects of these genes on osteogenic differentiation of hMSCs.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"97 4","pages":"209-218"},"PeriodicalIF":1.1,"publicationDate":"2022-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10373526","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}

{"title":"Whole-genome sequencing analysis of wild house mice (Mus musculus) captured in Madagascar.","authors":"Kazumichi Fujiwara,&nbsp;Marie C Ranorosoa,&nbsp;Satoshi D Ohdachi,&nbsp;Satoru Arai,&nbsp;Yuki Sakuma,&nbsp;Hitoshi Suzuki,&nbsp;Naoki Osada","doi":"10.1266/ggs.22-00090","DOIUrl":"https://doi.org/10.1266/ggs.22-00090","url":null,"abstract":"<p><p>In Madagascar, the house mouse (Mus musculus) is widely believed to have colonized with human activities and is now one of the most abundant rodents on the island. However, its genetic background at the genomic level remains unclear, and clarifying this would help us to infer the timing of introduction and route of migration. In this study, we determined the whole-genome sequences of five Madagascar house mice captured from an inland location in Madagascar. We examined the genetic background of samples by analyzing the mitochondrial and autosomal genomes. We confirmed that the mitochondrial genome lineages of collected samples formed a single clade placed at one of the most basal positions in the Mus musculus species. Autosomal genomic sequences revealed that these samples are most closely related to the subspecies M. m. castaneus (CAS), but also contain a genetic component of the subspecies M. m. domesticus (DOM). The signature of a strong population bottleneck 1,000-3,000 years ago was observed in both mitochondrial and autosomal genomic data. In a comparison with global samples of M. musculus, the Madagascar samples showed strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal and insular regions, with divergence time estimated as around 4,000 years ago. These findings support the proposition that the ancestors of these animals started to colonize the island with human agricultural activity and experienced a complex history during their establishment.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"97 4","pages":"193-207"},"PeriodicalIF":1.1,"publicationDate":"2022-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10390060","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}

{"title":"Environmental stress and transposons in plants.","authors":"Hidetaka Ito","doi":"10.1266/ggs.22-00045","DOIUrl":"https://doi.org/10.1266/ggs.22-00045","url":null,"abstract":"<p><p>Transposons were once thought to be junk repetitive DNA in the genome. However, their importance gradually became apparent as it became clear that they regulate gene expression, which is essential for organisms to survive, and that they are important factors in the driving force of evolution. Since there are multiple transposons in the genomes of all organisms, transposons have likely been activated and increased in copy number throughout their long history. This review focuses on environmental stress as a factor in transposon activation, paying particular attention to transposons in plants that are activated by environmental stresses. It is now known that plants respond to environmental stress in various ways, and correspondingly, many transposons respond to stress. The relationship between environmental stress and transposons is reviewed, including the mechanisms of their activation and the effects of transposon activation on host plants.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"97 4","pages":"169-175"},"PeriodicalIF":1.1,"publicationDate":"2022-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10749859","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}

{"title":"Euchromatin factors HULC and Set1C affect heterochromatin organization and mating-type switching in fission yeast Schizosaccharomyces pombe.","authors":"Alfredo Esquivel-Chávez,&nbsp;Takahisa Maki,&nbsp;Hideo Tsubouchi,&nbsp;Testuya Handa,&nbsp;Hiroshi Kimura,&nbsp;James E Haber,&nbsp;Geneviève Thon,&nbsp;Hiroshi Iwasaki","doi":"10.1266/ggs.22-00012","DOIUrl":"https://doi.org/10.1266/ggs.22-00012","url":null,"abstract":"<p><p>Mating-type (P or M) of fission yeast Schizosaccharomyces pombe is determined by the transcriptionally active mat1 cassette and is switched by gene conversion using a donor, either mat2 or mat3, located in an adjacent heterochromatin region (mating-type switching; MTS). In the switching process, heterochromatic donors of genetic information are selected based on the P or M cell type and on the action of two recombination enhancers, SRE2 promoting the use of mat2-P and SRE3 promoting the use of mat3-M, leading to replacement of the content of the expressed mat1 cassette. Recently, we found that the histone H3K4 methyltransferase complex Set1C participates in donor selection, raising the question of how a complex best known for its effects in euchromatin controls recombination in heterochromatin. Here, we report that the histone H2BK119 ubiquitin ligase complex HULC functions with Set1C in MTS, as mutants in the shf1, brl1, brl2 and rad6 genes showed defects similar to Set1C mutants and belonged to the same epistasis group as set1Δ. Moreover, using H3K4R and H2BK119R histone mutants and a Set1-Y897A catalytic mutant, we found that ubiquitylation of histone H2BK119 by HULC and methylation of histone H3K4 by Set1C are functionally coupled in MTS. Cell-type biases in MTS in these mutants suggested that HULC and Set1C inhibit the use of the SRE3 recombination enhancer in M cells, thus favoring SRE2 and mat2-P. Consistent with this, imbalanced switching in the mutants was traced to compromised association of the directionality factor Swi6 with the recombination enhancers in M cells. Based on their known effects at other chromosomal locations, we speculate that HULC and Set1C control nucleosome mobility and strand invasion near the SRE elements. In addition, we uncovered distinct effects of HULC and Set1C on histone H3K9 methylation and gene silencing, consistent with additional functions in the heterochromatic domain.</p>","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"97 3","pages":"123-138"},"PeriodicalIF":1.1,"publicationDate":"2022-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10114098","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}

{"title":"Role of Error Catastrophe in Transmission Ability of Virus","authors":"N. Takahata, Hirotaka Sugawara","doi":"10.1101/2022.06.28.22276997","DOIUrl":"https://doi.org/10.1101/2022.06.28.22276997","url":null,"abstract":"The role played by \"error catastrophe\" is explicitly taken into account in the mathematical formulation to analyze the COVID-19 data. The idea is to combine the mathematical genetics formalism of the error catastrophe of mutations in the virus gene loci with the standard model of epidemics which lacks the explicit incorporation of the mutation effect on the spreading of the viruses. We apply the formalism to the case of SARS-CoV-2 virus. We assume the \"universality\" of the error catastrophe in the process of analyzing the data. This means that some basic parameter to describe the error catastrophe is independent of which group (country or city) we deal with. Concretely, we analyze the omicron data of South Africa and then analyze the cases of Japan using the same value of the basic parameter derived in the South Africa analysis. The result shows the validity of our universality assumption.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":"1 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2022-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42333815","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}