Genes & genetic systems最新文献

Development and characterization of expressed sequence tag-simple sequence repeat markers for the near-threatened halophyte, Limonium tetragonum (Thunb.) A. A. Bullock (Plumbaginaceae). 针对濒危卤叶植物 Limonium tetragonum (Thunb.) A. A. Bullock（Plumbaginaceae）的表达序列标签-简单序列重复标记的开发和特征描述。

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-11-02 DOI: 10.1266/ggs.24-00093

Kako Ohbayashi, Naoko Ishikawa, Nonoka Takehara, Takahide Kurosawa, Yoshikuni Hodoki

引用次数: 0

Next-generation sequencing analysis with a population-specific human reference genome. 利用特定人群的人类参考基因组进行下一代测序分析。

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-10-28 DOI: 10.1266/ggs.24-00112

Tomohisa Suzuki, Kota Ninomiya, Takamitsu Funayama, Yasunobu Okamura, Shu Tadaka, Kengo Kinoshita, Masayuki Yamamoto, Shigeo Kure, Atsuo Kikuchi, Gen Tamiya, Jun Takayama

{"title":"Next-generation sequencing analysis with a population-specific human reference genome.","authors":"Tomohisa Suzuki, Kota Ninomiya, Takamitsu Funayama, Yasunobu Okamura, Shu Tadaka, Kengo Kinoshita, Masayuki Yamamoto, Shigeo Kure, Atsuo Kikuchi, Gen Tamiya, Jun Takayama","doi":"10.1266/ggs.24-00112","DOIUrl":"https://doi.org/10.1266/ggs.24-00112","url":null,"abstract":"Next-generation sequencing (NGS) has become widely available and is routinely used in basic research and clinical practice. The reference genome sequence is an essential resource for NGS analysis, and several population-specific reference genomes have recently been constructed to provide a choice to deal with the vast genetic diversity of human samples. However, resources supporting population-specific references are insufficient, and it is burdensome to perform analysis using these reference genomes. Here, we constructed a set of resources to support NGS analysis using the Japanese reference genome, JG. We created resources for variant calling, variant-effect prediction, gene and repeat element annotations, read mappability, and RNA-seq analysis. We also provide a resource for reference coordinate conversion for further annotation enrichment. We then provide a variant calling protocol with JG. Our resources provide a guide to prepare sufficient resources for the use of population-specific reference genomes and can facilitate the migration of reference genomes.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499053","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

FOXM1 derived from Triple negative breast cancer exosomes promotes cancer progression by activating IDO1 transcription in macrophages to suppress ferroptosis and induce M2 polarization of Tumor-associated macrophages. 三阴性乳腺癌外泌体中的 FOXM1 通过激活巨噬细胞中的 IDO1 转录来抑制铁变态反应并诱导肿瘤相关巨噬细胞的 M2 极化，从而促进癌症进展。

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-10-18 DOI: 10.1266/ggs.24-00079

Tielin Wang, Yan Zhang, Hong Liu, Jian Wu

{"title":"FOXM1 derived from Triple negative breast cancer exosomes promotes cancer progression by activating IDO1 transcription in macrophages to suppress ferroptosis and induce M2 polarization of Tumor-associated macrophages.","authors":"Tielin Wang, Yan Zhang, Hong Liu, Jian Wu","doi":"10.1266/ggs.24-00079","DOIUrl":"https://doi.org/10.1266/ggs.24-00079","url":null,"abstract":"To explore the oncogenic mechanism of FOXM1 in the tumor microenvironment (TME) regarding triple negative breast cancer (TNBC) promotion. The mRNA and protein levels of target genes in TNBC cells and their exosomes were detected by RT-qPCR and western blot. Co-culture models of TNBC cells and THP-1/M0 macrophages was established to detect the impact of co-culture on FOXM1 expression and macrophage polarization direction. The bioinformatics website was used to predict the binding sites between the FOXM1 and IDO1 promoter, which were further validated using dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay. Finally, after erastin-induced ferroptosis, Cell Counting Kit-8 (CCK-8), terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL), and other experiments were conducted to investigate whether the FOXM1/IDO1 axis regulates M2 macrophage polarization through ferroptosis. It was found that FOXM1 was highly expressed in exosomes derived from TNBC cells, and TNBC cells upregulated FOXM1 expression in THP-1 cells through exosomes to promote M2 macrophage polarization. Furthermore, FOXM1 upregulated IDO1 in M2-type TAMs by regulating transcription. Lastly, FOXM1/IDO1 inhibited ferroptosis, promoting M2 macrophage polarization, thereby advancing TNBC progression. In conclusions, FOXM1 derived from TNBC cell-derived exosomes activated IDO1 transcription in TAMs to inhibit ferroptosis, promoting TAMs' M2 polarization and exerting carcinogenic effects.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463195","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

Mutagenic effects of ultraviolet radiation and trimethyl psoralen in mycoplasma toward a minimal genome. 紫外线辐射和三甲基补骨脂素对支原体最小基因组的诱变作用

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-10-18 Epub Date: 2024-08-10 DOI: 10.1266/ggs.24-00061

Kaito Seo, Kensei Okada, Norikazu Ichihashi

{"title":"Mutagenic effects of ultraviolet radiation and trimethyl psoralen in mycoplasma toward a minimal genome.","authors":"Kaito Seo, Kensei Okada, Norikazu Ichihashi","doi":"10.1266/ggs.24-00061","DOIUrl":"10.1266/ggs.24-00061","url":null,"abstract":"Mycoplasmas, autonomously culturable bacteria with the smallest genome, are an important organism to understand the minimal form of life. Mutagenesis using mutagens is a useful methodology for understanding the essential regions of genomic information. Ultraviolet light (UV) and trimethyl psoralen (TMP) are mutagens known to induce various mutations; the latter is reported to specifically induce deletions in nematodes. However, their mutagenic effects on mycoplasma are not known. Here, we exposed Metamycoplasma salivarium to UV-C light or TMP and UV-A as mutagens, and analyzed the mutational pattern after serial cultivation ranging from 34 to 56 rounds for different lineages. Our results showed that more deletions, but fewer point mutations, were induced with TMP and UV-A than with UV-C, indicating the usefulness of TMP in inducing deletions. In addition, we compared our results with mutational data from other studies, which suggested that the combination of TMP and UV-A or UV-C exposure both induced point mutations that were highly biased toward C→T and G→A transitions. These data provide useful basic knowledge for mutational studies on M. salivarium.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970987","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

Identification of abiotic stress-responsive genes: a genome-wide analysis of the cytokinin response regulator gene family in rice. 鉴定非生物胁迫响应基因：水稻细胞分裂素响应调节基因家族的全基因组分析

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-09-18 Epub Date: 2024-06-29 DOI: 10.1266/ggs.24-00068

Setu Rani Saha, S M Shahinul Islam, Kimiko Itoh

{"title":"Identification of abiotic stress-responsive genes: a genome-wide analysis of the cytokinin response regulator gene family in rice.","authors":"Setu Rani Saha, S M Shahinul Islam, Kimiko Itoh","doi":"10.1266/ggs.24-00068","DOIUrl":"10.1266/ggs.24-00068","url":null,"abstract":"Response regulators (RRs) are implicated in various developmental processes as well as environmental responses by acting as either positive or negative regulators, and are crucial components of cytokinin signaling in plants. We characterized 36 RRs in rice (Oryza sativa L.; Os) using in silico analysis of publicly available data. A comprehensive analysis of OsRR family members covered their physicochemical properties, chromosomal distribution, subcellular localization, phylogeny, gene structure, distribution of conserved motifs and domains, and gene duplication events. Gene Ontology analysis indicated that 22 OsRR genes contribute mainly to the cytokinin response and signal transduction. Predicted cis-elements in RR promoter sequences related to phytohormones and abiotic stresses indicated that RRs are involved in hormonal and environmental responses, supporting previous studies. MicroRNA (miRNA) target analysis showed that 148 miRNAs target 29 OsRR genes. In some cases, multiple RRs are targets of the same miRNA group, and may be controlled by common stimulus responses. Based on the analysis of publicly available gene expression data, OsRR4, OsRR6, OsRR9, OsRR10, OsRR22, OsPRR73 and OsPRR95 were found to be involved in responses to abiotic stresses. Using quantitative reverse transcription polymerase chain reaction we confirmed that six of these RRs, namely OsRR4, OsRR6, OsRR9, OsRR10, OsRR22 and OsPRR73, are involved in the response to salinity, osmotic, alkaline and wounding stresses, and can potentially be used as models to understand molecular mechanisms underlying stress responsiveness.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467436","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

β-Tyrosine and its biosynthetic enzyme TAM1 are predominantly distributed in the ancestral subpopulation of japonica rice in Oryza rufipogon. β-酪氨酸及其生物合成酶 TAM1 主要分布在粳稻的祖先亚群 Oryza rufipogon 中。

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-09-13 Epub Date: 2024-07-19 DOI: 10.1266/ggs.24-00017

Shunta Sakamoto, Takanori Yoshikawa, Yutaka Sato, Naoki Mori

{"title":"β-Tyrosine and its biosynthetic enzyme TAM1 are predominantly distributed in the ancestral subpopulation of japonica rice in Oryza rufipogon.","authors":"Shunta Sakamoto, Takanori Yoshikawa, Yutaka Sato, Naoki Mori","doi":"10.1266/ggs.24-00017","DOIUrl":"10.1266/ggs.24-00017","url":null,"abstract":"Intraspecific variation in specialized metabolites plays a crucial role in the adaptive response to diverse environments. Two major subspecies, japonica and indica, are observed in Asian cultivated rice (Oryza sativa L.). Previously, we identified (3R)-β-tyrosine, a novel nonproteinogenic β-amino acid in plants, along with the enzyme tyrosine aminomutase (TAM1), which is required for β-tyrosine biosynthesis, in the japonica cultivar Nipponbare. Notably, TAM1 and β-tyrosine were preferentially distributed in japonica cultivars compared with indica cultivars. Considering its phytotoxicity and antimicrobial activity, intraspecific variation in β-tyrosine may contribute to the defensive potential of japonica rice. Investigation of the evolutionary trajectory of TAM1 and β-tyrosine should enhance our understanding of the evolution of rice defense. However, their distribution patterns in O. rufipogon, the direct ancestor of O. sativa, remain unclear. Therefore, in this study, we extensively examined TAM1 presence/absence and β-tyrosine content in 110 genetically and geographically diverse O. rufipogon accessions and revealed that they are characteristically observed in the ancestral subpopulation of japonica rice, while being absent or slightly accumulated in other subpopulations. Thus, we conclude that TAM1 and β-tyrosine in japonica rice are likely derived from its ancestral subpopulation. Furthermore, the high and low TAM1 possession rates and β-tyrosine content in japonica and indica rice, respectively, could be attributed to distribution patterns of TAM1 and β-tyrosine in their ancestral subpopulations. This study provides fundamental insights into the evolution of rice defense.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733869","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

Latitudinal adaptation and dispersal pathway of foxtail millet suggested by geographical distribution of transposable elements inserted in the SiPRR37 gene. 插入狐尾粟 SiPRR37 基因的转座元件的地理分布所提示的纬度适应性和扩散途径。

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-07-25 Epub Date: 2024-05-24 DOI: 10.1266/ggs.24-00023

Kenji Fukunaga, Akira Abe, Kazue Ito, Kaori Oikawa, Masaya Tsuji, Makoto Kawase

引用次数: 0

Development of polymorphic microsatellite markers for distylous-homostylous Primula secundiflora (Primulaceae) using HiSeq sequencing. 利用 HiSeq 测序技术开发多态性微卫星标记，用于二歧同株报春花（报春花科）。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2024-05-24 Epub Date: 2024-04-13 DOI: 10.1266/ggs.23-00340

Hua-Ying Sun, Wen-Ping Zhang, Wei Zhou, Zhi-Kun Wu, Lan-Ping Zheng

{"title":"Development of polymorphic microsatellite markers for distylous-homostylous Primula secundiflora (Primulaceae) using HiSeq sequencing.","authors":"Hua-Ying Sun, Wen-Ping Zhang, Wei Zhou, Zhi-Kun Wu, Lan-Ping Zheng","doi":"10.1266/ggs.23-00340","DOIUrl":"10.1266/ggs.23-00340","url":null,"abstract":"Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140331648","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

METTL21C mediates autophagy and formation of slow-twitch muscle fibers in mice after exercise. METTL21C 在运动后介导自噬的发生和慢肌纤维的形成。

IF 1 4区生物学

Genes & genetic systems Pub Date : 2024-05-10 Epub Date: 2024-04-18 DOI: 10.1266/ggs.23-00320

Jing Qu, Shuai Dang, Yuan-Yuan Sun, Tao Zhang, Hai Jiang, Hong-Zhao Lu

{"title":"METTL21C mediates autophagy and formation of slow-twitch muscle fibers in mice after exercise.","authors":"Jing Qu, Shuai Dang, Yuan-Yuan Sun, Tao Zhang, Hai Jiang, Hong-Zhao Lu","doi":"10.1266/ggs.23-00320","DOIUrl":"10.1266/ggs.23-00320","url":null,"abstract":"Homeostasis is essential for muscle repair and regeneration after skeletal muscle exercise. This study investigated the role of methyltransferase-like 21C (METTL21C) in skeletal muscle of mice after exercise and the potential mechanism. First, muscle samples were collected at 2, 4 and 6 weeks after exercise, and liver glycogen, muscle glycogen, blood lactic acid and triglyceride were assessed. Moreover, the expression levels of autophagy markers and METTL21C in skeletal muscle were analyzed. The results showed that the expression levels of METTL21C and MYH7 in the gastrocnemius muscle of mice in the exercise group were significantly higher after exercise than those in the control group, which suggested that long-term exercise promoted the formation of slow-twitch muscle fibers in mouse skeletal muscle. Likewise, the autophagy capacity was enhanced with the prolongation of exercise in muscles. The findings were confirmed in mouse C2C12 cells. We discovered that knockdown of Mettl21c reduced the expression of MYH7 and the autophagy level in mouse myoblasts. These findings indicate that METTL21C promotes skeletal muscle homeostasis after exercise by enhancing autophagy, and also contributes to myogenic differentiation and the formation of slow muscle fibers.","PeriodicalId":12690,"journal":{"name":"Genes & genetic systems","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989796","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

A budding yeast CAGE dataset comprising two cell types. 芽殖酵母帽分析两种细胞类型的基因表达数据集。

IF 1.1 4区生物学

Genes & genetic systems Pub Date : 2024-04-18 Epub Date: 2024-04-13 DOI: 10.1266/ggs.24-00020

Kei Kawakami, Shin-Ichi Maeda, Yoshiko Tanimoto, Mitsuhiro Shimizu, Hiroaki Kato

引用次数: 0