Genomics最新文献_第9页

De novo genome assembly and functional insights of the first commercial pink Auricularia cornea 首个商业化粉红耳廓藻角膜的全新基因组组装和功能研究。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-23 DOI: 10.1016/j.ygeno.2024.110902

Lei Ye , Lingzi Zhang , Xin Li , Yu Huang , Bo Zhang , Xuezhen Yang , Wei Tan , Xiaolin Li , Xiaoping Zhang

{"title":"De novo genome assembly and functional insights of the first commercial pink Auricularia cornea","authors":"Lei Ye , Lingzi Zhang , Xin Li , Yu Huang , Bo Zhang , Xuezhen Yang , Wei Tan , Xiaolin Li , Xiaoping Zhang","doi":"10.1016/j.ygeno.2024.110902","DOIUrl":"10.1016/j.ygeno.2024.110902","url":null,"abstract":"<div><p>A pioneering pink cultivar of <em>Auricularia cornea</em>, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink <em>A. cornea</em> Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink <em>A. cornea</em> genome and provides a comprehensive insight into its complex functions.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110902"},"PeriodicalIF":3.4,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400123X/pdfft?md5=e29e1581ba4c1349c90bca58b752a31d&pid=1-s2.0-S088875432400123X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758137","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

Genomic binding of NF-Y in mouse and human cells 小鼠和人类细胞中 NF-Y 的基因组结合。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-23 DOI: 10.1016/j.ygeno.2024.110895

Mirko Ronzio , Andrea Bernardini , Valentina Taglietti , Michele Ceribelli , Giacomo Donati , Alberto Gallo , Giulio Pavesi , Paolo Dellabona , Giulia Casorati , Graziella Messina , Roberto Mantovani , Diletta Dolfini

{"title":"Genomic binding of NF-Y in mouse and human cells","authors":"Mirko Ronzio , Andrea Bernardini , Valentina Taglietti , Michele Ceribelli , Giacomo Donati , Alberto Gallo , Giulio Pavesi , Paolo Dellabona , Giulia Casorati , Graziella Messina , Roberto Mantovani , Diletta Dolfini","doi":"10.1016/j.ygeno.2024.110895","DOIUrl":"10.1016/j.ygeno.2024.110895","url":null,"abstract":"<div><p>NF-Y is a Transcription Factor that regulates transcription through binding to the CCAAT-box. To understand its strategy, we analyzed 16 ChIP-seq datasets from human and mouse cells. Shared loci, mostly located in promoters of expressed genes of <em>cell cycle</em>, <em>metabolism</em> and <em>gene expression</em> pathways, are associated with histone marks of active chromatin and specific modules of TFs. Other peaks are in enhancers and Transposable Elements -TE- of retroviral origin in human and mouse. We evaluated the relationship with USF1, a common synergistic partner in promoters and MLT1 TEs, upon NF-YB inactivation: USF1 binding decreases in promoters, modestly in MLT1, suggesting a pioneering role of NF-Y in formers, not in the latters. These data define a common set of NF-Y functional targets across different mammalian cell types, suggesting a pioneering role in promoters with respect to TEs.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110895"},"PeriodicalIF":3.4,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001162/pdfft?md5=6850140a6102f7e5bec34cde46b029a4&pid=1-s2.0-S0888754324001162-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723398","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

Integrated morphological, physiological and transcriptomic analyses reveal the responses of Toona sinensis seedlings to low-nitrogen stress 综合形态学、生理学和转录组分析揭示了香椿幼苗对低氮胁迫的响应。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-22 DOI: 10.1016/j.ygeno.2024.110899

Hu Zhao, Miaomiao Ge, Fengzhe Zhang, Didi Du, Zilu Zhao, Cheng Shen, Qingping Hao, Min Xiao, Xiaopu Shi, Juan Wang, Mingqin Fan

{"title":"Integrated morphological, physiological and transcriptomic analyses reveal the responses of Toona sinensis seedlings to low-nitrogen stress","authors":"Hu Zhao, Miaomiao Ge, Fengzhe Zhang, Didi Du, Zilu Zhao, Cheng Shen, Qingping Hao, Min Xiao, Xiaopu Shi, Juan Wang, Mingqin Fan","doi":"10.1016/j.ygeno.2024.110899","DOIUrl":"10.1016/j.ygeno.2024.110899","url":null,"abstract":"<div><p>Nitrogen is one of the most essential elements for plant growth and development. In this study, the growth, physiology, and transcriptome of <em>Toona sinensis</em> (A. Juss) Roem seedlings were compared between low-nitrogen (LN) and normal-nitrogen (NN) conditions. These results indicate that LN stress adversely influences <em>T. sinensis</em> seedling growth. The activities of key enzymes related to nitrogen assimilation and phytohormone contents were altered by LN stress. A total of 2828 differentially expressed genes (DEGs) in roots and 1547 in leaves were identified between the LN and NN treatments. A differential enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that nitrogen and sugar metabolism, flavonoid biosynthesis, plant hormone signal transduction, and ABC transporters, were strongly affected by LN stress. In summary, this research provides information for further understanding the response of <em>T. sinensis</em> to LN stress.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110899"},"PeriodicalIF":3.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001204/pdfft?md5=8e7b6b59ffd47e6d24fc5ecafa41a27e&pid=1-s2.0-S0888754324001204-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758140","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

Deciphering cellular heterogeneity in Spodoptera frugiperda midgut cell line through single cell RNA sequencing 通过单细胞 RNA 测序破译弗氏蝶类中肠细胞系的细胞异质性。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-22 DOI: 10.1016/j.ygeno.2024.110898

Surjeet Kumar Arya , Douglas A. Harrison , Subba Reddy Palli

{"title":"Deciphering cellular heterogeneity in Spodoptera frugiperda midgut cell line through single cell RNA sequencing","authors":"Surjeet Kumar Arya , Douglas A. Harrison , Subba Reddy Palli","doi":"10.1016/j.ygeno.2024.110898","DOIUrl":"10.1016/j.ygeno.2024.110898","url":null,"abstract":"<div><p>Using the 10x Genomics Chromium single-cell RNA sequencing (scRNA-seq) platform, we discovered unexpected heterogeneity in an established cell line developed from the midgut of the Fall armyworm, <em>Spodoptera frugiperda,</em> a major global pest. We analyzed the sequences of 18,794 cells and identified ten unique cellular clusters, including stem cells, enteroblasts, enterocytes and enteroendocrine cells, characterized by the expression of specific marker genes. Additionally, these studies addressed an important knowledge gap by investigating the expression of genes coding for respiratory and midgut membrane insecticide targets classified by the Insecticide Resistance Action Committee. Dual-fluorescence tagging method, fluorescence microscopy and fluorescence-activated cell sorting confirmed the expression of midgut cell type-specific genes. Stem cells were isolated from the heterogeneous population of SfMG-0617 cells. Our results, validated by KEGG and Gene Ontology analyses and supported by Monocle 3.0, advance the fields of midgut cellular biology and establish standards for scRNA-seq studies in non-model organisms.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110898"},"PeriodicalIF":3.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001198/pdfft?md5=6846659334c462f6e93963047776ea48&pid=1-s2.0-S0888754324001198-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758138","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

Identification of differentially expressed genes in the medial prefrontal cortex of rats subjected to chronic unpredictable mild stress and treated with electroacupuncture 电针治疗大鼠内侧前额叶皮层中不同表达基因的鉴定。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-22 DOI: 10.1016/j.ygeno.2024.110901

Yujiao Zhang , Haiyan Zhang , Xinjie Zheng , Yi Hou , Xiaoli Chang , Lili Zhang , Ying Wang , Shaozong Chen

{"title":"Identification of differentially expressed genes in the medial prefrontal cortex of rats subjected to chronic unpredictable mild stress and treated with electroacupuncture","authors":"Yujiao Zhang , Haiyan Zhang , Xinjie Zheng , Yi Hou , Xiaoli Chang , Lili Zhang , Ying Wang , Shaozong Chen","doi":"10.1016/j.ygeno.2024.110901","DOIUrl":"10.1016/j.ygeno.2024.110901","url":null,"abstract":"<div><p>Major depressive disorder is a chronic mental health condition that seriously impacts afflicted individuals. Although electroacupuncture has proven to be an effective therapy for depression, its underlying biological mechanism remains largely unknown. In this study, we aimed to investigate the effects of electroacupuncture on depression-like behavior and to identify potential target genes related to those effects. To achieve this, we subjected rats to chronic unpredictable mild stress (CUMS) and used sucrose preference, forced swimming, and open-field tests to determine their depression-like behavior in the absence or after receipt of electroacupuncture treatment. RNA sequencing technology was then used to reveal the differentially expressed genes associated with depression and electroacupuncture treatment effects in the medial prefrontal cortex (mPFC). Repeated electroacupuncture treatments at the Baihui (GV20) and Taichong (LR3) acupoints significantly alleviated depression-like behavioral defects in the animals. Genomic RNA sequencing revealed several significant changes in the mPFC transcriptome of rats that received treatment. Through differential gene expression analysis, we found that electroacupuncture reversed the CUMS-induced downregulation of 46 genes and upregulation of 13 genes. Among the differentially expressed genes, <em>Casr</em>, <em>Bdkrb2</em>, <em>Gnb3</em>, and <em>Ccl1</em> were found to be associated with depression and electroacupuncture treatment effects. In conclusion, we verified that electroacupuncture treatment has an effective antidepressant effect, and the underlying mechanism involves multiple systems and targets.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110901"},"PeriodicalIF":3.4,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001228/pdfft?md5=2548044293fb3e8dd1813b4216bdb241&pid=1-s2.0-S0888754324001228-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758139","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

Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea) 重复元件扩增是 Pamphagidae 基因组大小巨大化的原因之一：一项比较研究（直翅目，Acridoidea）。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-19 DOI: 10.1016/j.ygeno.2024.110896

Yimeng Nie, Xuanzeng Liu, Lina Zhao, Yuan Huang

{"title":"Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea)","authors":"Yimeng Nie, Xuanzeng Liu, Lina Zhao, Yuan Huang","doi":"10.1016/j.ygeno.2024.110896","DOIUrl":"10.1016/j.ygeno.2024.110896","url":null,"abstract":"<div><p>Pamphagidae is a family of Acridoidea that inhabits the desert steppes of Eurasia and Africa. This study employed flow cytometry to estimate the genome size of eight species in the Pamphagidae. The results indicate that the genome size of the eight species ranged from 13.88 pg to 14.66 pg, with an average of 14.26 pg. This is the largest average genome size recorded for the Orthoptera families, as well as for the entire Insecta. Furthermore, the study explored the role of repetitive sequences in the genome, including their evolutionary dynamics and activity, using low-coverage next-generation sequencing data. The genome is composed of 14 different types of repetitive sequences, which collectively make up between 59.9% and 68.17% of the total genome. The Pamphagidae family displays high levels of transposable element (TE) activity, with the number of TEs increasing and accumulating since the family's emergence. The study found that the types of repetitive sequences contributing to the TE outburst events are similar across species. Additionally, the study identified unique repetitive elements for each species. The differences in repetitive sequences among the eight Pamphagidae species correspond to their phylogenetic relationships. The study sheds new light on genome gigantism in the Pamphagidae and provides insight into the correlation between genome size and repetitive sequences within the family.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110896"},"PeriodicalIF":3.4,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001174/pdfft?md5=b3d96f38f32a82b26dfe6c684a5ee84b&pid=1-s2.0-S0888754324001174-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723399","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

Assembly and comparative analysis of the complete mitochondrial genome of Vaccinium carlesii Dunn Dunn Vaccinium carlesii 完整线粒体基因组的组装和比较分析。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-18 DOI: 10.1016/j.ygeno.2024.110897

Liwei Chu , Qianhui Du , Siyu Zuo , Guiting Liu , Hexin Wang , Guoling Liu , Lina Zhao , Guohui Xu

{"title":"Assembly and comparative analysis of the complete mitochondrial genome of Vaccinium carlesii Dunn","authors":"Liwei Chu , Qianhui Du , Siyu Zuo , Guiting Liu , Hexin Wang , Guoling Liu , Lina Zhao , Guohui Xu","doi":"10.1016/j.ygeno.2024.110897","DOIUrl":"10.1016/j.ygeno.2024.110897","url":null,"abstract":"<div><p><em>Vaccinium</em> L. is an important fruit tree with nutritional, medicinal, and ornamental values. However, the mitochondrial (mt) genome of <em>Vaccinium</em> L. remains largely unexplored. <em>Vaccinium carlesii</em> Dunn is an endemic wild resource in China, which is crucial for blueberry breeding. The <em>V. carlesii</em> mt genomes were sequenced using Illumina and Nanopore, which total length was 636,904 bp with 37 protein coding genes, 20 tRNA genes, and three rRNA genes. We found four pairs of long repeat fragments homologous recombination mediated the generation of substructures in the <em>V. carlesii</em> mt genome. We predicted 383 RNA editing sites, all converting cytosine (C) to uracil (U). According to the phylogenetic analysis, <em>V. carlesii</em> and <em>V. macrocarpon</em> of the Ericaceae exhibited the closest genetic relationship. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of <em>Vaccinium</em> germplasm resources.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110897"},"PeriodicalIF":3.4,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001186/pdfft?md5=39eb0d5485e6035017c04f3f09a2a092&pid=1-s2.0-S0888754324001186-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733924","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

Complex chromosomal 6q rearrangements revealed by combined long-molecule genomics technologies 长分子基因组学联合技术揭示了复杂的染色体 6q 重排。

IF 3.4 2区生物学

Genomics Pub Date : 2024-07-15 DOI: 10.1016/j.ygeno.2024.110894

Sachiko Ohori , Hironao Numabe , Satomi Mitsuhashi , Naomi Tsuchida , Yuri Uchiyama , Eriko Koshimizu , Kohei Hamanaka , Kazuharu Misawa , Satoko Miyatake , Takeshi Mizuguchi , Atsushi Fujita , Naomichi Matsumoto

{"title":"Complex chromosomal 6q rearrangements revealed by combined long-molecule genomics technologies","authors":"Sachiko Ohori , Hironao Numabe , Satomi Mitsuhashi , Naomi Tsuchida , Yuri Uchiyama , Eriko Koshimizu , Kohei Hamanaka , Kazuharu Misawa , Satoko Miyatake , Takeshi Mizuguchi , Atsushi Fujita , Naomichi Matsumoto","doi":"10.1016/j.ygeno.2024.110894","DOIUrl":"10.1016/j.ygeno.2024.110894","url":null,"abstract":"<div><p>Technologies for detecting structural variation (SV) have advanced with the advent of long-read sequencing, which enables the validation of SV at a nucleotide level. Optical genome mapping (OGM), a technology based on physical mapping, can also provide comprehensive SVs analysis. We applied long-read whole genome sequencing (LRWGS) to accurately reconstruct breakpoint (BP) segments in a patient with complex chromosome 6q rearrangements that remained elusive by conventional karyotyping. Although all BPs were precisely identified by LRWGS, there were two possible ways to construct the BP segments in terms of their orders and orientations. Thus, we also used OGM analysis. Notably, OGM recognized entire inversions exceeding 500 kb in size, which LRWGS could not characterize. Consequently, here we successfully unveil the full genomic structure of this complex chromosomal 6q rearrangement and cryptic SVs through combined long-molecule genomic analyses, showcasing how LRWGS and OGM can complement each other in SV analysis.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110894"},"PeriodicalIF":3.4,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001150/pdfft?md5=7b1d2689c4656d8f47c738a43098330e&pid=1-s2.0-S0888754324001150-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141633149","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

Unraveling the signaling pathways of phytohormones underlying salt tolerance in Elymus sibiricus: A transcriptomic and metabolomic approach 揭示西双版纳杓兰耐盐性所依赖的植物激素信号通路：转录组学和代谢组学方法

IF 3.4 2区生物学

Genomics Pub Date : 2024-06-27 DOI: 10.1016/j.ygeno.2024.110893

Ying De, Weihong Yan, Fengqin Gao, Huaibin Mu

{"title":"Unraveling the signaling pathways of phytohormones underlying salt tolerance in Elymus sibiricus: A transcriptomic and metabolomic approach","authors":"Ying De, Weihong Yan, Fengqin Gao, Huaibin Mu","doi":"10.1016/j.ygeno.2024.110893","DOIUrl":"10.1016/j.ygeno.2024.110893","url":null,"abstract":"<div><p>Understanding phytohormonal signaling is crucial for elucidating plant defense mechanisms against environmental stressors. However, knowledge regarding phytohormone-mediated tolerance pathways under salt stress in <em>Elymus sibiricus</em>, an important species for forage and ecological restoration, remains limited. In this study, transcriptomic and metabolomic approaches uncover the dynamics of phytohormonal signaling in <em>Elymus sibiricus</em> under salt stress. Notably, four hours after exposure to salt, significant activity was observed in the ABA, JA, IAA, and CTK pathways, with ABA, JA, JA-L-Ile, and IAA identified as key mediators in the response of <em>Elymus sibiricus</em>' to salinity. Moreover, SAPK3, Os04g0167900-like, CAT1, MKK2, and MPK12 were identified as potential central regulators within these pathways. The complex interactions between phytohormones and DEGs are crucial for facilitating the adaptation of <em>Elymus sibiricus</em> to saline environments. These findings enhance our understanding of the salt tolerance mechanisms in <em>Elymus sibiricus</em> and provide a foundation for breeding salt-resistant varieties.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110893"},"PeriodicalIF":3.4,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001149/pdfft?md5=deff24d321fb2fa39c0599eb1753062c&pid=1-s2.0-S0888754324001149-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467376","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

FOXCUT regulates the malignant phenotype of triple-negative breast Cancer via the miR-337-3p/ANP32E Axis FOXCUT通过miR-337-3p/ANP32E轴调节三阴性乳腺癌的恶性表型

IF 3.4 2区生物学

Genomics Pub Date : 2024-06-27 DOI: 10.1016/j.ygeno.2024.110892

Lei Shi, Ziwen Zhang, Yuan Huang, Yabing Zheng

{"title":"FOXCUT regulates the malignant phenotype of triple-negative breast Cancer via the miR-337-3p/ANP32E Axis","authors":"Lei Shi, Ziwen Zhang, Yuan Huang, Yabing Zheng","doi":"10.1016/j.ygeno.2024.110892","DOIUrl":"10.1016/j.ygeno.2024.110892","url":null,"abstract":"<div><h3>Background</h3><p>The lack of specific molecular targets and the rapid spread lead to a worse prognosis of triple-negative breast cancer (TNBC). Therefore, identifying new therapeutic and prognostic biomarkers helps to develop effective treatment strategies for TNBC.</p></div><div><h3>Methods</h3><p>Through preliminary bioinformatics analysis, FOXCUT was found to be significantly overexpressed in breast cancer, especially in TNBC. Tissue samples were collected from 15 TNBC patients, and qRT-PCR was employed to validate the expression of FOXCUT in both TNBC patient tissues and TNBC cell lines. We also carried out the GSEA analysis and KEGG enrichment analysis of FOXCUT. Additionally, the effects of FOXCUT knockdown on TNBC cell malignant behaviors, and aerobic glycolysis were assessed by methods including CCK-8, Transwell, western blot, and Seahorse XF 96 analyses. Moreover, utilizing databases predicting interactions between ceRNAs, corresponding lncRNA-miRNA binding relationships, and miRNA-mRNA interactions were predicted. These predictions were subsequently validated through RNA immunoprecipitation and dual-luciferase reporter assays.</p></div><div><h3>Results</h3><p>FOXCUT exhibited high expression in both TNBC tissues and cell lines, fostering cell malignant behaviors and glycolysis. FOXCUT was found to sponge miR-337-3p, while miR-337-3p negatively regulated the expression of ANP32E. Consequently, FOXCUT ultimately facilitated the malignant phenotype of TNBC by upregulating ANP32E expression.</p></div><div><h3>Conclusion</h3><p>This study elucidated the role of FOXCUT in elevating aerobic glycolysis levels in TNBC and driving malignant cancer cell development via the miR-337-3p/ANP32E regulatory axis.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110892"},"PeriodicalIF":3.4,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001137/pdfft?md5=f6b04dfe47c32ddb895f237ec04491a6&pid=1-s2.0-S0888754324001137-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467375","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