Genes & genetic systems最新文献_第9页

Mechanisms and impacts of genomic changes that are mediated by repetitive sequences in eukaryotes. 真核生物中由重复序列介导的基因组变化的机制和影响。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2023-01-01 DOI: 10.1266/ggs.98.101

Mariko Sasaki

引用次数: 0

GGS Prize 2023. 2023年GGS奖。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2023-01-01 DOI: 10.1266/ggs.98.207

引用次数: 0

How to establish a mutually beneficial relationship between a transposon and its host: lessons from Tam3 in Antirrhinum. 如何在转座子和宿主之间建立互惠互利的关系:来自安提林的Tam3的教训。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-12-17 DOI: 10.1266/ggs.22-00063

Shasha Wang, Yohei Koide, Yuji Kishima

{"title":"How to establish a mutually beneficial relationship between a transposon and its host: lessons from Tam3 in Antirrhinum.","authors":"Shasha Wang, Yohei Koide, Yuji Kishima","doi":"10.1266/ggs.22-00063","DOIUrl":"https://doi.org/10.1266/ggs.22-00063","url":null,"abstract":"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.","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}

引用次数: 0

Stress-responsive retrotransposable elements in conifers. 针叶树的应力响应逆转录因子。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-12-17 DOI: 10.1266/ggs.22-00042

Tokuko Ujino-Ihara

引用次数: 0

Time series clustering analysis of genes during osteogenic differentiation of human mesenchymal stem cells. 人间充质干细胞成骨分化过程基因的时间序列聚类分析。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-12-17 DOI: 10.1266/ggs.22-00068

Yaqiong Li, Jun Wang

{"title":"Time series clustering analysis of genes during osteogenic differentiation of human mesenchymal stem cells.","authors":"Yaqiong Li, Jun Wang","doi":"10.1266/ggs.22-00068","DOIUrl":"https://doi.org/10.1266/ggs.22-00068","url":null,"abstract":"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.","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}

引用次数: 1

Whole-genome sequencing analysis of wild house mice (Mus musculus) captured in Madagascar. 在马达加斯加捕获的野生家鼠(小家鼠)的全基因组测序分析。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-12-17 DOI: 10.1266/ggs.22-00090

Kazumichi Fujiwara, Marie C Ranorosoa, Satoshi D Ohdachi, Satoru Arai, Yuki Sakuma, Hitoshi Suzuki, Naoki Osada

{"title":"Whole-genome sequencing analysis of wild house mice (Mus musculus) captured in Madagascar.","authors":"Kazumichi Fujiwara, Marie C Ranorosoa, Satoshi D Ohdachi, Satoru Arai, Yuki Sakuma, Hitoshi Suzuki, Naoki Osada","doi":"10.1266/ggs.22-00090","DOIUrl":"https://doi.org/10.1266/ggs.22-00090","url":null,"abstract":"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.","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}

引用次数: 1

Environmental stress and transposons in plants. 植物中的环境胁迫与转座子。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-12-17 DOI: 10.1266/ggs.22-00045

Hidetaka Ito

引用次数: 5

Screening of biomarkers associated with diagnosis and prognosis of colorectal cancer. 结直肠癌诊断和预后相关生物标志物的筛选。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-10-18 Epub Date: 2022-09-15 DOI: 10.1266/ggs.21-00072

Mingfu Cui, Haiyan Zhang, Songyun Han, Feng Huo, Zhaoming Shen, Dayong Ding

{"title":"Screening of biomarkers associated with diagnosis and prognosis of colorectal cancer.","authors":"Mingfu Cui, Haiyan Zhang, Songyun Han, Feng Huo, Zhaoming Shen, Dayong Ding","doi":"10.1266/ggs.21-00072","DOIUrl":"https://doi.org/10.1266/ggs.21-00072","url":null,"abstract":"We aimed to explore biomarkers associated with diagnosis and prognosis of colorectal cancer. Differentially expressed protein (DEP) genes were obtained and validated. Moreover, co-expressed genes were screened and their prognostic value was evaluated. In addition, miRNAs that were negatively correlated with DEP genes were identified and used to construct a competitive endogenous RNA network. Furthermore, a support vector machine model was built using DEP genes, and a receiver operating characteristic curve was implemented to confirm its prediction performance. The results showed that only one DEP gene, CCL26, was obtained. Moreover, 43 genes co-expressed with CCL26 were identified, among which six (AP3M2, DAPK1, ISYNA1, PPM1K, PRR4 and RNF122) were linked with the prognosis of colorectal cancer. Besides, the axis RP11-47122.2/RP11-527N22.1-hsa-miR-3192-5p-CCL26 was identified as an lncRNA-miRNA-target gene network. Support vector machine model analysis showed that the area under the curve of CCL26 reached 0.878 based on GEO data and 0.743 based on our protein data. In conclusion, AP3M2, DAPK1, ISYNA1, PPM1K, PRR4, RNF122, CCL26 and hsa-miR-3192-5p appear to be related to the progression of colorectal cancer.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":"101-110"},"PeriodicalIF":1.1,"publicationDate":"2022-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40355418","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: 2

Temporal dynamics of mildly deleterious nonsynonymous substitutions in mitochondrial gene sequences in rodents and moles. 啮齿类动物和鼹鼠线粒体基因序列中轻度有害的非同义替换的时间动力学。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-10-18 Epub Date: 2022-06-25 DOI: 10.1266/ggs.21-00079

Yuta Inoue, Hitoshi Suzuki

{"title":"Temporal dynamics of mildly deleterious nonsynonymous substitutions in mitochondrial gene sequences in rodents and moles.","authors":"Yuta Inoue, Hitoshi Suzuki","doi":"10.1266/ggs.21-00079","DOIUrl":"https://doi.org/10.1266/ggs.21-00079","url":null,"abstract":"We have previously estimated the evolutionary rate (number of substitutions/site/million years) of mitochondrial cytochrome b gene (Cytb) sequences in rodents and moles to be about 0.11 at more recent divergence times of tens of thousands of years, and to decrease rapidly to about 0.03 at more distant divergence times. Because this time dependency is thought to be caused by the removal of mildly deleterious substitutions in later generations, we focused in this study on the abundance of nonsynonymous substitutions. We collected 23 haplogroups of Cytb with signals of late Quaternary population expansion events from rodents and moles and categorized them into three groups for comparison based on predicted expansion start time: 5,000-15,000 years ago (Group I), ca. 53,000 years ago (Group II) and 130,000-230,000 years ago (Group III). We counted the numbers of nonsynonymous and synonymous substitutions in all haplogroups. The rates of nonsynonymous substitutions were lowest in Groups II and III (0.08-0.22), whereas those in Group I varied markedly. We further classified Group I into two subgroups based on high (0.29-0.43) and low (0.09-0.20) nonsynonymous substitution rates, which were likely to be associated with the start of the expansion within 10,000 years and at around 15,000 years ago, respectively. The Group II and III networks had two- or three-step star-shaped structures and tended to exhibit frequent and less frequent nonsynonymous substitutions on exterior and interior branches, respectively. Based on temporal dynamics, nonsynonymous mitochondrial DNA (mtDNA) substitutions in small mammals accounted for at most 40% of all substitutions during the early evolutionary stage and then rapidly declined, dropping to approximately 15%. The results of this study provide a good explanation of the time-dependent trend in the mtDNA evolution rate predicted in previous work.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":"111-121"},"PeriodicalIF":1.1,"publicationDate":"2022-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40398734","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: 1

Construction of a massive genetic resource by transcriptome sequencing and genetic characterization of Megasyllis nipponica (Annelida: Syllidae). 利用转录组测序和遗传特征构建庞大的遗传资源。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2022-10-18 Epub Date: 2022-09-06 DOI: 10.1266/ggs.21-00137

Yoshinobu Hayashi, Kohei Oguchi, Mayuko Nakamura, Shigeyuki Koshikawa, Toru Miura

{"title":"Construction of a massive genetic resource by transcriptome sequencing and genetic characterization of Megasyllis nipponica (Annelida: Syllidae).","authors":"Yoshinobu Hayashi, Kohei Oguchi, Mayuko Nakamura, Shigeyuki Koshikawa, Toru Miura","doi":"10.1266/ggs.21-00137","DOIUrl":"https://doi.org/10.1266/ggs.21-00137","url":null,"abstract":"Understanding the processes and consequences of the morphological diversity of organisms is one of the major goals of evolutionary biology. Studies on the evolution of developmental mechanisms of morphologies, or evo-devo, have been extensively conducted in many taxa and have revealed many interesting phenomena at the molecular level. However, many other taxa exhibiting intriguing morphological diversity remain unexplored in the field of evo-devo. Although the annelid family Syllidae shows spectacular diversity in morphological development associated with reproduction, its evo-devo study, especially on molecular development, has progressed slowly. In this study, we focused on Megasyllis nipponica as a new model species for evo-devo in syllids and performed transcriptome sequencing to develop a massive genetic resource, which will be useful for future molecular studies. From the transcriptome data, we identified candidate genes that are likely involved in morphogenesis, including genes involved in hormone regulation, sex determination and appendage development. Furthermore, a computational analysis of the transcriptome sequence data indicated the occurrence of DNA methylation in coding regions of the M. nipponica genome. In addition, flow cytometry analysis showed that the genome size of M. nipponica was approximately 524 megabases. These results facilitate the study of morphogenesis in molecular terms and contribute to our understanding of the morphological diversity in syllids.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":" ","pages":"153-166"},"PeriodicalIF":1.1,"publicationDate":"2022-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40355520","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: 1