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Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer 元基因组分析揭示了肠道微生物组对晚期直肠癌新辅助放化疗反应的影响。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-15 DOI: 10.1016/j.ygeno.2024.110951
Hao Chen , Meizi Zeng , Syeda Sundas Batool , Yiming Zhao , Zheng Yu , Jumei Zhou , Ke Liu , Jing Huang
Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.
新辅助化放疗可提高晚期直肠癌患者的生存率,但其疗效差异很大。以往的研究表明,肠道微生物可作为预测治疗效果的生物标志物。然而,肠道微生物组在对 nCRT 反应良好的患者中的具体作用仍不清楚。本研究采用枪式元基因组测序技术分析了对nCRT有不同反应的患者的粪便微生物组。我们的研究结果表明,有益肠道细菌和不同代谢途径(碳水化合物代谢、氨基酸代谢和硫代谢)的基因在反应良好的患者中明显富集。此外,我们还阐明了微生物衍生的 GDP-D 鼠李糖和丁酸盐影响 nCRT 反应的因果关系。我们的研究结果为了解晚期结直肠癌患者对 nCRT 的不同反应提供了新的见解,并为提高晚期结直肠癌患者 nCRT 的疗效提供了有价值的参考。
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引用次数: 0
Integration analysis of transcriptome and metabolome revealed the potential mechanism of spermatogenesis in Tibetan sheep (Ovis aries) at extreme high altitude 转录组和代谢组的整合分析揭示了极高海拔地区藏绵羊精子发生的潜在机制。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-09 DOI: 10.1016/j.ygeno.2024.110949
Miaoshu Zhang , Xuejiao An , Chao Yuan , Tingting Guo , Binpeng Xi , Jianbin Liu , Zengkui Lu
Testis has an indispensable function in male reproduction of domestic animals. Numerous genes and metabolites were related to testicular development and spermatogenesis. However, little is known about the biological regulation pathways associated with fecundity in male Tibetan sheep. In this study, Testes were collected from Huoba Tibetan sheep (HB, 4614 m) and Gangba Tibetan sheep (GB, 4401 m) at extreme high altitude, and Alpine Merino sheep (AM, 2500 m, control group) at medium-high altitude, investigating the genes and metabolites levels of them. The histological analysis of testicular tissue using hematoxylin-eosin (HE) staining was performed for Tibetan sheep and Alpine Merino sheep, and the testes of them were analyzed by transcriptomics and metabolomics to explore the potential mechanism of testicular development and spermatogenesis. The statistical results showed that the cross-sectional area of testicular seminiferous tubules, diameter of seminiferous tubules, and spermatogenic epithelium thickness were significantly smaller in HB and GB than in AM (P < 0.05). Overall, 5648 differentially expressed genes (DEGs) and 336 differential metabolites (DMs) were identified in three sheep breeds, which were significantly enriched in spermatogenesis and other related pathways. According to integrated metabolomic and transcriptomic analysis, glycolysis/gluconeogenesis, AMPK signaling pathway, and TCA cycle, were predicted to have dramatic effects on the spermatogenesis of Tibetan sheep. Several genes (including Wnt2, Rab3a, Sox9, Hspa8, and Slc38a2) and metabolites (including L-histidinol, Glucose, Fumaric acid, Malic acid, and Galactose) were significantly enriched in pathways related to testicular development and spermatogenesis, and might affect the reproduction of Tibetan sheep by regulating the acrosome reaction, meiotic gene expression, and the production of sex hormones. Our results provide further understanding of the key genes and metabolites involved in testicular development and spermatogenesis in Tibetan sheep.
睾丸在家畜雄性生殖过程中具有不可或缺的功能。许多基因和代谢物与睾丸发育和精子生成有关。然而,人们对与雄性藏羊繁殖力相关的生物调控途径知之甚少。本研究采集了极高海拔的霍巴藏羊(HB,海拔4614米)和岗巴藏羊(GB,海拔4401米)以及中高海拔的高山美利奴羊(AM,海拔2500米,对照组)的睾丸,研究了它们的基因和代谢物水平。利用苏木精-伊红(HE)染色法对藏系绵羊和高山美利奴羊的睾丸组织进行组织学分析,并通过转录组学和代谢组学对其睾丸进行分析,以探索睾丸发育和精子发生的潜在机制。统计结果显示,HB 和 GB 的睾丸曲细精管横截面积、曲细精管直径和生精上皮厚度均显著小于 AM(P<0.05)。
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引用次数: 0
Analysis of genetic evolutionary differences among four Tibetan pig populations in China 中国四个藏猪种群的遗传进化差异分析
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-09 DOI: 10.1016/j.ygeno.2024.110950
Yiting Yang , Mailin Gan , Chengming Liu , Zhongwei Xie , Meng Wang , Chengpeng Zhou , Wenqiang Cheng , Lei Chen , Shunhua Zhang , Ye Zhao , Lili Niu , Yan Wang , Jingyong Wang , Linyuan Shen , Li Zhu
Tibetan pigs are a locally bred domestic pig breed originating from the Tibetan Plateau in China. They can be categorized into four distinct groups based on their geographical locations: Sichuan Tibetan pigs, Tibetan pigs from Tibet, Yunnan Tibetan pigs, and Gansu Tibetan pigs. This study aimed to explore population diversity, genetic structure and selection signals among Tibetan pigs in four Chinese national nature reserves. The results show that there is different observed heterozygosity among Tibetan pig populations (0.1957–0.1978). Ratio of runs of homozygosity (Froh) calculation of four Tibetan pig populations by runs of homozygosity (ROH) revealed the presence of inbreeding within the population (0.0336–0.0378). Analysis of the genetic structure demonstrated distinct population stratification among the four Tibetan pig populations, with each showing relatively independent evolutionary directions. Furthermore, Five methods (FST, Piratio, ROD, Tajima's D, XP-CLR) were used to artificially select evolutionary trajectories. The results mainly involved processes such as DNA repair, immune regulation, muscle fat deposition and adaptation to hypoxia. In conclusion, this study enhances our understanding of the genetic characteristics of Tibetan pig populations and provides a theoretical reference for the conservation of resources across different populations of Tibetan pigs.
藏香猪是原产于中国青藏高原的当地饲养的家猪品种。根据地理位置,它们可分为四个不同的群体:四川藏香猪、西藏藏香猪、云南藏香猪和甘肃藏香猪。本研究旨在探讨中国四个国家级自然保护区藏香猪的种群多样性、遗传结构和选择信号。结果表明,藏猪种群间存在不同的杂合度(0.1957-0.1978)。对四个藏猪种群的同种异交率(ROH)进行计算,发现种群内存在近交现象(0.0336-0.0378)。遗传结构分析表明,四个藏猪种群之间存在明显的种群分层,每个种群都呈现出相对独立的进化方向。此外,还利用五种方法(FST、Piratio、ROD、Tajima's D、XP-CLR)对进化轨迹进行了人工选择。结果主要涉及 DNA 修复、免疫调节、肌肉脂肪沉积和缺氧适应等过程。总之,本研究加深了我们对藏香猪种群遗传特征的了解,为藏香猪不同种群间的资源保护提供了理论参考。
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引用次数: 0
Comparative transcriptome analysis and identification of candidate bZIP transcription factors involved in anthraquinone biosynthesis in Rheum officinale Baill 参与大黄蒽醌生物合成的候选 bZIP 转录因子的转录组比较分析和鉴定
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-09 DOI: 10.1016/j.ygeno.2024.110948
Jing Tang , Yi-min Li , Yan Wang , Feng Yan , Zhao Feng , Rui-hua LV , Jing Gao , Liang Peng , Xiao-chen Hu , Gang Zhang
Rhubarb is a traditional medicinal plant in China, whose pharmacological effects derive mainly from its anthraquinones. However, the regulatory mechanism affecting anthraquinone biosynthesis in R. officinale remains poorly understood. We assembled a high-quality, full-length transcriptome using single-molecule real-time (SMRT) sequencing. 274 unigenes potentially involved in the biosynthesis of anthraquinones, including those in the shikimate, polyketide, MVA and MEP pathways, were identified based on full-length transcriptome. Differentially expressed genes (DEGs) induced by MeJA treatment and DEGs between different tissues were identified through next-generation sequencing (NGS), revealing the genes that may be involved in the biosynthesis of anthraquinones. The basic leucine zipper (bZIP) transcription factors of R. officinale were systematically identified. Key genes such as RobZIP50 and RobZIP53 were systematically identified and found to be associated with anthraquinone biosynthesis in R. officinale through differential expression, co-expression and protein interaction analyses. RobZIP50 and RobZIP53 were highly expressed in roots and rhizomes, and significantly increased after 12 h of MeJA treatment. Additionally, both RobZIP50 and RobZIP53 were localized exclusively in the nucleus, with RobZIP53 showing significant transcriptional activity. Taken together, our results suggest that RobZIP53 may play a role in regulating anthraquinone biosynthesis in R. officinale.
大黄是中国的传统药用植物,其药理作用主要来源于其蒽醌类化合物。然而,人们对影响大黄蒽醌生物合成的调控机制仍然知之甚少。我们利用单分子实时(SMRT)测序技术构建了高质量的全长转录组。根据全长转录组确定了 274 个可能参与蒽醌类化合物生物合成的单基因,包括莽草酸、多酮、MVA 和 MEP 途径中的单基因。通过新一代测序(NGS)鉴定了MeJA处理诱导的差异表达基因(DEGs)和不同组织间的差异表达基因,揭示了可能参与蒽醌类化合物生物合成的基因。系统鉴定了欧当归的碱性亮氨酸拉链(bZIP)转录因子。通过差异表达、共表达和蛋白质相互作用分析,系统鉴定了 RobZIP50 和 RobZIP53 等关键基因,发现它们与 R. officinale 的蒽醌生物合成有关。RobZIP50 和 RobZIP53 在根和根茎中高表达,并在 MeJA 处理 12 小时后显著增加。此外,RobZIP50和RobZIP53都只定位于细胞核中,其中RobZIP53表现出显著的转录活性。综上所述,我们的研究结果表明,RobZIP53 可能在调控 R. officinale 的蒽醌生物合成中发挥作用。
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引用次数: 0
The molecular regulated mechanism of METTL3 and FTO in lipid metabolism of Hu sheep METTL3和FTO在胡羊脂质代谢中的分子调控机制
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-27 DOI: 10.1016/j.ygeno.2024.110945
Bowen Chen , Chao Yuan , Tingting Guo , Jianbin Liu , Bohui Yang , Zengkui Lu

Background

Balanced lipid metabolism can improve the growth performance and meat quality of livestock. The m6A methylation-related genes METTL3 and FTO play important roles in animal lipid metabolism; however, the mechanism through which they regulate lipid metabolism in sheep is unclear.

Results

We established lipid deposition models of hepatocytes and preadipocytes in Hu sheep. In the hepatocyte lipid deposition model, the genes expression levels of FABP4, Accα, ATGL and METTL3, METTL14, and FTO—were significantly up-regulated after lipid deposition (P < 0.05). Transcriptomic and metabolomic analyses showed that lipid deposition had a significant effect on MAPK, steroid biosynthesis, and glycerophospholipid metabolism pathway in hepatocytes. The m6A methylation level decreased but the difference was not significant after METTL3 interference, and the expression levels of FABP4 and ATGL increased significantly (P < 0.05); the m6A methylation level significantly increased following METTL3 overexpression, and LPL and ATGL expression levels significantly decreased (P < 0.05), indicating that overexpression of METTL3 inhibited the expression of lipid deposition-related genes in a m6A-dependent manner. The m6A methylation level was significantly increased, ATGL expression was significantly decreased (P < 0.05), and LPL, FABP4, and Accα expression was not significantly changed following FTO interference (P > 0.05); the m6A methylation level was significantly decreased after FTO overexpression, and LPL, FABP4, and ATGL expression was significantly increased (P < 0.05), indicating that FTO overexpression increased the expression of lipid deposition-related genes in a m6A-dependent manner. Transcriptomic and metabolomic analyses showed that m6A methylation modification mainly regulated lipid metabolism through triglyceride metabolism, adipocytokine signaling, MAPK signaling, and fat digestion and absorption in hepatocytes. In the lipid deposition model of preadipocytes, the regulation of gene expression is the same as that in hepatocytes.

Conclusions

METTL3 significantly inhibited the expression of lipid deposition-related genes, whereas FTO overexpression promoted lipid deposition. Our study provides a theoretical basis and reference for accurately regulating animal lipid deposition by mastering METTL3 and FTO genes to promote high-quality animal husbandry.
背景:均衡的脂质代谢可以提高家畜的生长性能和肉质。m6A甲基化相关基因METTL3和FTO在动物脂质代谢中发挥重要作用,但它们调控绵羊脂质代谢的机制尚不清楚:结果:我们在胡羊体内建立了肝细胞和前脂肪细胞脂质沉积模型。在肝细胞脂质沉积模型中,脂质沉积后 FABP4、Accα、ATGL 和 METTL3、METTL14、FTO 的基因表达水平显著上调(P 0.05);FTO 过表达后 m6A 甲基化水平显著降低,LPL、FABP4 和 ATGL 表达显著升高(P 结论:METTL3、METTL14 和 FTO 对肝细胞脂质沉积有显著抑制作用:METTL3 能明显抑制脂质沉积相关基因的表达,而 FTO 过表达能促进脂质沉积。我们的研究为通过掌握 METTL3 和 FTO 基因准确调控动物脂质沉积,促进优质畜牧业的发展提供了理论依据和参考。
{"title":"The molecular regulated mechanism of METTL3 and FTO in lipid metabolism of Hu sheep","authors":"Bowen Chen ,&nbsp;Chao Yuan ,&nbsp;Tingting Guo ,&nbsp;Jianbin Liu ,&nbsp;Bohui Yang ,&nbsp;Zengkui Lu","doi":"10.1016/j.ygeno.2024.110945","DOIUrl":"10.1016/j.ygeno.2024.110945","url":null,"abstract":"<div><h3>Background</h3><div>Balanced lipid metabolism can improve the growth performance and meat quality of livestock. The m6A methylation-related genes <em>METTL3</em> and <em>FTO</em> play important roles in animal lipid metabolism; however, the mechanism through which they regulate lipid metabolism in sheep is unclear.</div></div><div><h3>Results</h3><div>We established lipid deposition models of hepatocytes and preadipocytes in Hu sheep. In the hepatocyte lipid deposition model, the genes expression levels of <em>FABP4</em>, Accα, <em>ATGL</em> and <em>METTL3</em>, <em>METTL14</em>, and <em>FTO</em>—were significantly up-regulated after lipid deposition (<em>P</em> &lt; 0.05). Transcriptomic and metabolomic analyses showed that lipid deposition had a significant effect on MAPK, steroid biosynthesis, and glycerophospholipid metabolism pathway in hepatocytes. The m6A methylation level decreased but the difference was not significant after <em>METTL3</em> interference, and the expression levels of <em>FABP4</em> and <em>ATGL</em> increased significantly (<em>P</em> &lt; 0.05); the m6A methylation level significantly increased following <em>METTL3</em> overexpression, and <em>LPL</em> and <em>ATGL</em> expression levels significantly decreased (<em>P</em> &lt; 0.05), indicating that overexpression of <em>METTL3</em> inhibited the expression of lipid deposition-related genes in a m6A-dependent manner. The m6A methylation level was significantly increased, <em>ATGL</em> expression was significantly decreased (<em>P</em> &lt; 0.05), and <em>LPL</em>, <em>FABP4</em>, and <em>Accα</em> expression was not significantly changed following <em>FTO</em> interference (<em>P</em> &gt; 0.05); the m6A methylation level was significantly decreased after <em>FTO</em> overexpression, and <em>LPL</em>, <em>FABP4</em>, and <em>ATGL</em> expression was significantly increased (<em>P</em> &lt; 0.05), indicating that <em>FTO</em> overexpression increased the expression of lipid deposition-related genes in a m6A-dependent manner. Transcriptomic and metabolomic analyses showed that m6A methylation modification mainly regulated lipid metabolism through triglyceride metabolism, adipocytokine signaling, MAPK signaling, and fat digestion and absorption in hepatocytes. In the lipid deposition model of preadipocytes, the regulation of gene expression is the same as that in hepatocytes.</div></div><div><h3>Conclusions</h3><div><em>METTL3</em> significantly inhibited the expression of lipid deposition-related genes, whereas <em>FTO</em> overexpression promoted lipid deposition. Our study provides a theoretical basis and reference for accurately regulating animal lipid deposition by mastering <em>METTL3</em> and <em>FTO</em> genes to promote high-quality animal husbandry.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110945"},"PeriodicalIF":3.4,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Definition of regulatory elements and transcription factors controlling porcine immune cell gene expression at single cell resolution using single nucleus ATAC-seq 利用单核 ATAC-seq 以单细胞分辨率确定控制猪免疫细胞基因表达的调控元件和转录因子。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-24 DOI: 10.1016/j.ygeno.2024.110944
Pengxin Yang , Ryan Corbett , Lance Daharsh , Juber Herrera Uribe , Kristen A. Byrne , Crystal L. Loving , Christopher Tuggle
The transcriptome of porcine peripheral blood mononuclear cells (PBMC) at single cell (sc) resolution is well described, but little is understood about the cis-regulatory mechanism behind scPBMC gene expression. Here, we profiled the open chromatin landscape of porcine PBMC that define cis-regulatory elements and mechanism contributing to the transcription using single nucleus ATAC sequencing (snATAC-seq). Approximately 22 % of the identified peaks overlapped with annotated transcription start sites (TSS). Using clustering based on open chromatin pattern similarity, we demonstrate that cell type annotations using snATAC-seq are highly concordant to that reported for sc RNA sequencing (scRNA-seq). The differentially accessible peaks (DAPs) for each cell type were characterized and the pattern of accessibility of the DAPs near cell type markers across cell types was similar to that of the average gene expression level of corresponding marker genes. Additionally, we found that peaks identified in snATAC-seq have the potential power to predict the cell type specific transcription starting site (TSS). We identified both transcription factors (TFs) whose binding motif were enriched in cell type DAPs of multiple cell types and cell type specific TFs by conducting transcription factor binding motif (TFBM) analysis. Furthermore, we identified the putative enhancer or promoter regions bound by TFs for each differentially expressed gene (DEG) with a DAP that overlapped with its TSS by generating cis-co-accessibility networks (CCAN). To predict the regulators of such DEGs, TFBM analysis was performed for each CCAN. The regulator TF-target DEG pairs predicted in this way were largely consistent with the results reported in the ENCODE Transcription Factor Targets Dataset (TFTD). This snATAC-seq approach provides insights into the regulation of chromatin accessibility landscape of porcine PBMCs and enables discovery of TFs predicted to control DEG through binding regulatory elements whose chromatin accessibility correlates with the DEG promoter region.
单细胞(sc)分辨率的猪外周血单核细胞(PBMC)转录组已经得到了很好的描述,但对scPBMC基因表达背后的顺式调控机制却知之甚少。在这里,我们利用单核 ATAC 测序(snATAC-seq)分析了猪 PBMC 的开放染色质图谱,以确定顺式调控元件和转录机制。鉴定出的峰值中约有 22% 与注释的转录起始位点(TSS)重叠。通过基于开放染色质模式相似性的聚类,我们证明使用 snATAC-seq 进行的细胞类型注释与 sc RNA 测序(scRNA-seq)报告的注释高度一致。我们对每种细胞类型的差异可及峰(DAP)进行了表征,不同细胞类型细胞类型标记附近的差异可及峰的可及性模式与相应标记基因的平均基因表达水平相似。此外,我们发现在 snATAC-seq 中发现的峰具有预测细胞类型特定转录起始位点(TSS)的潜在能力。我们通过进行转录因子结合基序(TFBM)分析,确定了其结合基序在多种细胞类型 DAPs 中富集的转录因子(TFs)和细胞类型特异性 TFs。此外,我们还通过生成顺式-逆式可及性网络(CCAN),为每个DAP与其TSS重叠的差异表达基因(DEG)确定了与TF结合的增强子或启动子区域。为了预测这些 DEG 的调控因子,对每个 CCAN 进行了 TFBM 分析。通过这种方法预测的调节因子-靶标 DEG 对与 ENCODE 转录因子靶标数据集(TFTD)中报告的结果基本一致。这种snATAC-seq方法有助于深入了解猪PBMCs染色质可及性的调控情况,并能发现预测通过结合染色质可及性与DEG启动子区域相关的调控元件来控制DEG的TFs。
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引用次数: 0
Whole-genome resequencing and RNA-seq analysis implicates GPR75 as a potential genetic basis related to retarded growth in South China carp (Cyprinus carpio rubrofuscus) 全基因组重测序和 RNA-seq 分析表明,GPR75 是华南鲤生长迟缓的潜在遗传基础。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.ygeno.2024.110934
Zaixuan Zhong , Jiajia Fan , Yuanyuan Tian , Minhui Lin , Huaping Zhu , Dongmei Ma
The south China carp (Cyprinus carpio rubrofuscus) is an indigenous and important fish species, widely cultured in south China. However, part of individuals experienced retarded growth, the genetic basis of which has yet to be elucidated. In this study, whole-genome resequencing of 35 fast-growing and 35 retarded-growing south China carp were conducted to identify promising genes associated with retarded growth. Twelve candidate SNPs were detected and annotated to the Gpr75 gene, which has been reported to be related with body weight through regulating insulin homeostasis. RNA-seq analysis of muscle suggested that differentially expressed genes were significantly enriched in the insulin signaling pathway. Additionally, the fasting serum insulin level was significantly lower while the blood glucose level was significantly higher in the retarded-growing group. Our preliminary study provides insights into the genetic basis underlying the retarded growth and may facilitate further genetic improvement of south China carp.
华南鲤(Cyprinus carpio rubrofuscus)是一种重要的土著鱼类,在中国南方被广泛养殖。然而,部分个体出现生长迟缓现象,其遗传基础尚未阐明。本研究对35条生长迅速和35条生长迟缓的华南鲫鱼进行了全基因组重测序,以确定与生长迟缓相关的潜在基因。研究发现了12个候选SNPs,并将其注释到Gpr75基因上,据报道该基因通过调节胰岛素平衡与体重有关。肌肉的RNA-seq分析表明,胰岛素信号通路中显著富集了差异表达基因。此外,生长迟缓组的空腹血清胰岛素水平明显降低,而血糖水平明显升高。我们的初步研究揭示了华南鲤生长迟缓的遗传基础,可能有助于华南鲤的进一步遗传改良。
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引用次数: 0
Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper 窥探缝隙:长读测序揭示了澳大利亚鲷鱼的结构变异和基因组进化。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.ygeno.2024.110929
Julie Blommaert , Jonathan Sandoval-Castillo , Luciano B. Beheregaray , Maren Wellenreuther

Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.

甚至在基因组测序之前,遗传资源就已经为物种管理和育种计划提供了支持。目前的技术,如长线程测序,可以解析复杂的基因组区域,如富含重复序列或高 GC 含量的区域。基因组连续性的改善提高了鉴定结构变异(SV)和转座元件(TE)的准确性。我们展示了经过改进的澳大利亚鲷鱼(Chrysophrys auratus)基因组组装和 SV 目录。新的基因组序列更加连续,可以确定 14 个中心粒,并从黄鳍鲷中转移了 26,115 个基因注释。与之前的基因组相比,新的基因组注释增加了 35,000 个 SV,包括更大和更复杂的重排。SV 和 TE 的分布模式偏向染色体末端,这可能是受重组的影响。一些 SV 与生长相关基因重叠,突出了它们的重要性。这一升级基因组为研究自然选择和人工选择奠定了基础,为相关物种提供了参考,并揭示了进化过程中基因组的动态变化。
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引用次数: 0
Multiomics reveals blood differential metabolites and differential genes in the early onset of ketosis in dairy cows 多组学揭示了奶牛酮病早期发病过程中的血液差异代谢物和差异基因。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.ygeno.2024.110927
Sha Ping , Ma Xuehu , Hu Chunli, Feng Xue, An Yanhao, Ma Yun, Ma Yanfen

Ketosis—a metabolic state characterized by elevated levels of ketone bodies in the blood or urine—reduces the performance and health of dairy cows and causes substantial economic losses for the dairy industry. Currently, beta-hydroxybutyric acid is the gold standard for determining ketosis in cows; however, as this method is only applicable postpartum, it is not conducive to the early intervention of ketosis in dairy cows. In this study, the sera of dry, periparturient, postpartum ketotic, and healthy cows were analyzed by both transcriptomics and metabolomics techniques. Moreover, changes of gene expression and metabolites were observed, and serum physiological and biochemical indexes were detected by ELISA. The purpose was to screen biomarkers that can be used to detect the incidence of dry or periparturient ketosis in cows. The results showed that ketotic cows had increased levels of glycolipid metabolism indexes, oxidizing factors, and inflammatory factors during dry periods and liver damage, which could be used as early biomarkers to predict the onset of ketosis. Transcriptomic results yielded 20 differentially expressed genes (DEGs) between ketotic and healthy cows during dry, peripartum, and postpartum periods. GO and KEGG enrichment analyses indicated that these DEGs were involved in amino acid metabolism, energy metabolism, and disease-related signaling pathways. The metabolomics sequencing results showed that ketotic cows mainly showed enrichment in tricarboxylic acid cycle, butyric acid metabolism, carbon metabolism, lysine degradation, fatty acid degradation, and other signaling pathways. Metabolites differed between ketotic and healthy cows in dry, pre-parturition, and post-parturition periods. Combined transcriptomics and metabolomics analyses identified significant enrichment in the glucagon signaling pathway and the lysine degradation signaling pathway in dry, periparturient, and postpartum ketotic cows. PRKAB2 and SETMAR—key DEGs of the glucagon signaling pathway and lysine degradation signaling pathway, respectively—can be used as key marker genes for determining the early onset of ketosis in dairy cows.

酮病--一种以血液或尿液中酮体水平升高为特征的代谢状态--会降低奶牛的生产性能和健康水平,并给乳品业造成巨大的经济损失。目前,β-羟丁酸是确定奶牛酮病的黄金标准;然而,由于这种方法仅适用于产后,因此不利于对奶牛酮病进行早期干预。本研究采用转录组学和代谢组学技术分析了干奶牛、围产期奶牛、产后酮病奶牛和健康奶牛的血清。此外,还观察了基因表达和代谢物的变化,并通过 ELISA 检测了血清生理生化指标。目的是筛选出可用于检测奶牛干性或围产期酮病发病率的生物标志物。结果表明,酮病奶牛的糖脂代谢指标、氧化因子和炎症因子水平在干奶期和肝损伤期均有所升高,这些指标可作为预测酮病发生的早期生物标志物。转录组学结果显示,在干燥期、围产期和产后,酮病奶牛和健康奶牛之间存在20个差异表达基因(DEGs)。GO和KEGG富集分析表明,这些DEGs涉及氨基酸代谢、能量代谢和疾病相关信号通路。代谢组学测序结果显示,酮症奶牛主要在三羧酸循环、丁酸代谢、碳代谢、赖氨酸降解、脂肪酸降解和其他信号通路中表现出富集。酮病奶牛和健康奶牛在干奶、产前和产后的代谢物存在差异。结合转录组学和代谢组学分析发现,在干奶、围产期和产后酮症奶牛中,胰高血糖素信号通路和赖氨酸降解信号通路显著富集。PRKAB2和SETMAR--分别是胰高血糖素信号通路和赖氨酸降解信号通路的关键DEG--可作为确定奶牛酮病早期发病的关键标记基因。
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引用次数: 0
STRIP2 is regulated by the transcription factor Sp1 and promotes lung adenocarcinoma progression via activating the PI3K/AKT/mTOR/MYC signaling pathway STRIP2 受转录因子 Sp1 的调控,通过激活 PI3K/AKT/mTOR/MYC 信号通路促进肺腺癌的进展。
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.ygeno.2024.110923
Junfan Pan , Yuan Zhang , Liu He , Yue Wu , Weijin Xiao , Jing Zhang , Yiquan Xu

Background

Patients with lung adenocarcinoma (LUAD) generally have poor prognosis. The role of striatin-interacting protein 2 (STRIP2) in LUAD remain unclear.

Methods

Liquid chromatography-mass spectrometry analyses were used to screen the STRIP2-binding proteins and co-immunoprecipitation verified these interactions. A dual luciferase reporter assay explored the transcription factor activating STRIP2 transcription. Xenograft and lung metastasis models assessed STRIP2's role in tumor growth and metastasis in vivo.

Results

STRIP2 is highly expressed in LUAD tissues and is linked to poor prognosis. STRIP2 expression in LUAD cells significantly promoted cell proliferation, invasion, and migration in vitro and in vivo. Mechanistically, STRIP2 boosted the PI3K/AKT/mTOR/MYC cascades by binding AKT. In addition, specificity protein 1, potently activated STRIP2 transcription by binding to the STRIP2 promoter. Blocking STRIP2 reduces tumor growth and lung metastasis in xenograft models.

Conclusions

Our study identifies STRIP2 is a key driver of LUAD progression and a potential therapeutic target.

背景:肺腺癌(LUAD)患者一般预后较差。纹蛋白相互作用蛋白 2(STRIP2)在 LUAD 中的作用仍不清楚:方法:利用液相色谱-质谱分析筛选 STRIP2 结合蛋白,并通过共沉淀验证这些相互作用。双荧光素酶报告实验探索了激活STRIP2转录的转录因子。异种移植和肺转移模型评估了STRIP2在体内肿瘤生长和转移中的作用:结果:STRIP2在LUAD组织中高表达,并与预后不良有关。STRIP2在LUAD细胞中的表达能显著促进细胞在体外和体内的增殖、侵袭和迁移。从机制上讲,STRIP2通过结合AKT促进了PI3K/AKT/mTOR/MYC级联反应。此外,特异性蛋白 1 通过与 STRIP2 启动子结合,有效激活了 STRIP2 的转录。在异种移植模型中,阻断STRIP2可减少肿瘤生长和肺转移:我们的研究发现 STRIP2 是 LUAD 进展的关键驱动因素和潜在治疗靶点。
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引用次数: 0
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