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Long Noncoding RNA Expression Signatures of Abdominal Aortic Aneurysm Revealed by Microarray

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Biomedical and Environmental Sciences 2016年第10期29卷 713-723页

作者： YANG Yao Guo LI Mei Xia KOU Lei ZHOU You QIN Yan Wen LIU Xiao Jun CHEN Zhong The Department of Vascular Surgery Beijing Anzhen Hospital Capital Medical University Beijing 100029 China State Key Laboratory of Brain and Cognitive Science Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China State Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical Sciences ＆ School of Basic Medicine Peking Union Medical College Beijing 100005 China

Objective This study is aimed at observing the role of long noncoding RNAs（lncR NAs） in the pathogenesis of abdominal aortic aneurysm（AAA）.Methods Lnc RNA and m RNA expression signatures of AAA tissues and normal abdominal aortic tissues（NT） were analyzed by microarray and further verified by Real-time quantitative reverse-transcription PCR（q RT-PCR）.The lnc RNAs-m RNAs targeting relationships were identified using computational analysis.The effect of lnc-ARG on 5-lipoxygenase（ALOX5） expression was tested in HeL a cells.Results Differential expressions of 3,688 lncR NAs and 3,007 m RNAs were identified between AAA and NT tissues.Moreover,1,284 differentially expressed long intergenic noncoding RNAs and 206 differentially expressed enhancer-like lnc RNAs adjacent to protein-coding genes were discerned by bioinformatics analysis.Some differentially expressed lncR NAs and m RNAs between AAA and normal tissue samples were further verified using q RT-PCR.A co-expression network of coding and noncoding genes was constructed based on the correlation analysis between the differentially expressed lnc RNAs and mR NAs.In addition,the lnc-ARG located within the upstream of ALOX5 was sorted as a noncoding transcript by analyzing the protein-coding potential using computational analysis.Furthermore,we found that lnc-ARG can decrease the m RNA level of ALOX5 and reactive oxygen species production in He La cells.Conclusion This study revealed new lnc RNA candidates are related to the pathogenesis of AAA.

关键词： incrna Abdominal aortic aneurysm Inc-ARG ALOX5

Long Non-coding RNAs in the Cytoplasm

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Genomics, Proteomics & Bioinformatics 2016年第2期14卷 73-80页

作者： Farooq Rashid Abdullah Shah Ge Shan CAS Key Laboratory of Innate Immunity and Chronic Disease CAS Center for Excellence in Molecular Cell ScienceSchool of Life Sciences University of Science and Technology of China

An enormous amount of long non-coding RNAs（lnc RNAs） transcribed from eukaryotic genome are important regulators in different aspects of cellular events. Cytoplasm is the residence and the site of action for many lncRNAs. The cytoplasmic lncRNAs play indispensable roles with multiple molecular mechanisms in animal and human cells. In this review, we mainly talk about functions and the underlying mechanisms of lncRNAs in the cytoplasm. We highlight relatively well-studied examples of cytoplasmic lncRNAs for their roles in modulating mRNA stability,regulating m RNA translation, serving as competing endogenous RNAs, functioning as precursors of microRNAs, and mediating protein modifications. We also elaborate the perspectives of cytoplasmic lncRNA studies.

关键词： incrna mRNA stability mRNA translation ceRNA MicroRNA

LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency

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Journal of Molecular Cell Biology 2021年第4期13卷 295-313页

作者： Pixi Yan Yuyang Lu Jing Niu Juntao Gao Michael Q.Zhang Yafei Yin Xiaohua Shen Tsinghua-Peking joint Center for Life Sciences School of Medicine and School of Life SciencesTsinghua UniversityBeijingChina Department of Cell Biology Zhejiang University School of MedicineHangzhouChina t These authors contributed equally to this work

Super-enhancers(SEs)comprise large clusters of enhancers,which are co-occupied by multiple lineage-specific and master tran-scription factors,and play pivotal roles in regulating gene expression and cell fate determination.However,it is still largely un-known whether and how SEs are regulated by the noncoding portion of the genome.Here,through genome-wide analysis,wefound that tpng noncoding RNA(incrna)genes preferentially lie next to SEs.In mouse embryonic stem cells(mESCs),depletionof$E-associated IlncRNA transcripts dysregulated the activity of their nearby SEs.Specifically,we revealed a critical regulatoryrole of the incrna gene Platr22 in modulating the activity of a nearby SE and the expression of the nearby pluripotency regulatorZFP281.Through these regulatory events,Platr22 contributes to pluripotency maintenance and proper differentiation of mESCs.Mechanistically,Platr22 transcripts coat chromatin near the SE region and interact with DDX5 and hnRNP-L.DDX5 further recruitsp300 and other factors related to active transcription.We propose that these factors assemble into a transcription hub,thus pro-moting an open and active epigenetic chromatin state.0ur study highlights an unanticipated role for a class of lncRNAs in epige-netically controlling the activity and vulnerability to perturbation of nearby SEs for cell fate determination.

关键词： incrna Platr22t super-enhancer pluripotency

Transcriptional identification of differentially expressed genes associated with division of labor in Apis cerana cerana

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Insect Science 2021年第2期28卷 457-471页

作者： Yi-Jie Chen Ying-Jiao Li Shuang Wu Wen-Chao Yang Jing Miao Shao-Hua Gu Jiang-Hong Li Xiao-Qing Miao Xianchun Li College of Bee Science Fujian Agriculture and Forestry UniversityFuzhouChina State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina Department of Entomology and BI05 Institute University of ArizonaTucsonAZUSA

Workers of Apis cerana cerana undergo an in-hive nursing to outdoor foraging transition,but the genes underlying this age-related transition remain largely unknown.Here,we sequenced the head transcriptomes of its 7-day-old normal nurses,18-and 22-day-old normal foragers,7-day-old precocious foragers and 22-day-old over-aged nurses to unravel the genes associated with this transition.Mapping of the sequence reads to Apis mellifera genome showed that the three types of foragers had a greater percentage of reads from annotated exons and intergenic regions,whereas the two types of nurses had a greater percentage of reads from introns.Pair-and group-wise comparisons of the five transcriptomes revealed 59 uniquely expressed genes(18 in nurses and 41 in foragers)and 14 nurse-and 15 forager-upregulated genes.The uniquely expressed genes are usually low-abundance long noncoding RNAs,transcription factors,transcription coactivators,RNA-binding proteins,kinases or phosphatases that are involved in signaling and/or regulation,whereas the nurse-or forager-upregulated genes are often high-abundance downstream genes that directly perform the tasks of nurses or foragers.Taken together,these results suggest that the nurse-forager transition is coordinated by a social signal-triggered epigenetic shift from introns to exons/intergenic regions and the resulting transcriptional shift between the nurse-and forager-associated genes.

关键词： behavioral transition epigenetic shift incrna over-aged nurses precocious foragers signaling genes

Long non-coding RNA Databases in Cardiovascular Research

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Genomics, Proteomics & Bioinformatics 2016年第4期14卷 191-199页

作者： Frank Rühle Monika Stoll Institute of Human Genetics Genetic EpidemiologyUniversity of Muenster48149 MuensterGermany Carmany Cardiovascular Research Institute Maastricht(CARIM) Genetic Epidemiology and Statistical GeneticsMaastricht Center for Systems Biology(MaCSBio)Maastricht University6211 LK MaastrichtThe Netherlands

With the rising interest in the regulatory functions of long non-coding RNAs （incrnas） in complex human diseases such as cardiovascular diseases, there is an increasing need in public databases offering comprehensive and integrative data for all aspects of these versatile molecules. Recently, a variety of public data repositories that specialized in lncRNAs have been developed, which make use of huge high-throughput data particularly from next-generation sequencing （NGS） approaches. Here, we provide an overview of current incrna databases covering basic and functional annotation, incrna expression and regulation, interactions with other biomolecules, and genomic variants influencing the structure and function of lncRNAs. The prominent incrna antisense noncoding RNA in the INK4 locus （ANRIL）, which has been unequivocally associated with coronary artery disease through genome-wide association studies （GWAS）, serves as an example to demonstrate the features of each individual database.

关键词： Database Non-coding incrna Gene regulation Cardiovascular disease ANRIL

Progress and prospects of noncoding RNAs in insects

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Journal of Integrative Agriculture 2019年第4期18卷 729-747页

作者： LI Mei-zhen XIAO Hua-mei HE Kang LI Fei Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects Institute of Insect Sciences College of Agriculture and Biotechnology Zhejiang University College of Life Sciences and Resource Environment Yichun University

With the rapid development of high-throughput sequencing technology and bioinformatics algorithms, great progress has been made in the field of noncoding RNA(ncRNA) in the last decade. RNA molecules have been regarded only as a messenger between DNA and protein for decades, but now they have new roles in the biological process as ncRNAs. A growing number of ncRNAs have been identified in insects from the RNA-Seq data of small RNA libraries or transcriptomes. ncRNAs have varied regulatory functions at the epigenetic, transcriptional, or post-transcriptional levels, and participate in almost all types of biological processes. Here, we review the research progress of four kinds of ncRNAs, including microRNA(miRNA), Piwiinteracting RNA(piRNA), circular RNA(circRNA), and long noncoding RNA(lncRNA) in insects. The discovery, biogenesis mechanisms, and regulatory functions of these ncRNAs are presented here to provide a comprehensive understanding of insect ncRNAs and to promote the application of ncRNAs in insect pest control.

关键词： miRNA piRNA circRNA incrna biogenesis prediction regulatory functions

miR-155过表达髓核细胞incrna表达谱芯片分析及对凋亡功能的影响

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中国老年学杂志 2018年第10期38卷 2430-2432页

作者：覃国忠史鹏亮张震霍少川广州中医药大学广东广州510000

目的探讨在椎间盘退变过程中miR-155过表达髓核细胞incrna对凋亡功能的影响及机制。方法采用miR-155慢病毒载体过表达人椎间盘细胞髓核细胞,incrna芯片检测并通过基因组数据库(Ensemble)筛选出可能通过miR-155参与髓核细胞凋亡调控的Inc... 详细信息

目的探讨在椎间盘退变过程中miR-155过表达髓核细胞incrna对凋亡功能的影响及机制。方法采用miR-155慢病毒载体过表达人椎间盘细胞髓核细胞,incrna芯片检测并通过基因组数据库(Ensemble)筛选出可能通过miR-155参与髓核细胞凋亡调控的incrna;将筛选出的GAS5 incrna转染髓核细胞,流式细胞术检测过表达GAS5 incrna后髓核细胞的凋亡情况;Western印迹法检测线粒体通路上两个关键凋亡相关蛋白含半胱氨酸的天冬氨酸蛋白水解酶(Caspase)-3和B淋巴细胞瘤/白血病(Bcl)-2的表达情况。结果经incrna芯片分析共发现630个差异表达incrna,其中381个incrna表达上调、249个incrna表达下调。Ensemble显示,GAS5 incrna共包含有30个转录本,本次incrna芯片分析获得了13个转录本表达情况,均呈下降趋势,其中GAS5-016转录下调差异有统计学意义(Fc值≥1.5,Pincrna过表达髓核细胞后,流式细胞术分析显示,GAS5 incrna过表达组髓核细胞早期凋亡率明显高于阴性对照组(Pincrna过表达组髓核细胞中Caspase-3蛋白表达水平明显高于阴性对照组,Bcl-2蛋白表达水平明显低于阴性对照组(均Pincrna在人退变椎间盘髓核细胞凋亡中发挥重要作用,GAS5 incrna过表达可上调Caspase-3表达并下调Bcl-2表达同时激活细胞内的线粒体凋亡通路,促进髓核细胞凋亡;miR-155可能参与了GAS5 incrna调控髓核细胞凋亡的过程,但二者的相互调控机制仍需进一步研究。

关键词： incrna 椎间盘退变髓核细胞凋亡

lncRNA基因芯片技术筛选膝骨性关节炎差异性基因表达的构建研究

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中文科技期刊数据库（全文版）医药卫生 2023年第6期 43-45页

作者：曾文丛赣州市人民医院江西赣州341000

利用基因芯片技术对膝骨性关节炎差异表达的长链非编码RNA(incrna)进行初步筛选,同时对其生物学功能和相关代谢通路进行分析,以期为膝骨性关节的治疗提供参考。方法研究对象选择我院2020年12月~2022年12月收治的膝骨性关节炎患者作为... 详细信息

利用基因芯片技术对膝骨性关节炎差异表达的长链非编码RNA(incrna)进行初步筛选,同时对其生物学功能和相关代谢通路进行分析,以期为膝骨性关节的治疗提供参考。方法研究对象选择我院2020年12月~2022年12月收治的膝骨性关节炎患者作为观察组,选择同期健康体检者作为对照组,各39例。抽取两组研究对象外周静脉血样本利用incrna基因芯片进行检测,对差异基因进行筛选和分析,确定差异基因和差异incrna及其相关生物学功能和信号通路。结果两组研究对象中共筛选出1760个具有差异性的mRNA表达基因,其中上调和下调的mRNA 个数分别有360个和1370个;两组研究对象中共筛选出2250个具有差异性的incrna表达基因,其中上调和下调的incrna 个数分别有620个和1670个;两组差异表达的incrnas主要涉及到参与金属离子结合、细胞组分、蛋白结合、病毒转录、rRNA过程等;通过高级分析最终筛选出的具有显著差异的incrna有68个,其FC值均>4,其中上调和下调的基因数分别有7个和65个,分别占总数的10.29%和89.71%。与骨性关节分发病相关的incrna主要为Inc-HERC-6-3、Inc-FAM3B-8、Inc-SERPINCI 。KEGC分析结果显示,Wnt通路、NF-κB信号通路和细胞黏附分子(CAMs)为主要参与的通路。靶基因结果显示,膝骨性关节炎的发病中参与的主要为incrnas MEG3和incrnaa CIR。结论:通过基因芯片技术筛选出1760个具有差异性的mRNA表达基因和2250个具有差异性的incrna表达基因,靶基因结果显示膝骨性关节炎的发病中参与的2条incrnas主要为incrnas MEG3和incrnaa CIR,该研究结果为膝骨性关节炎的发病机制的和靶向治疗的研究提供参考。

关键词：膝骨性关节炎基因差异 incrna

lncRNA在原发性肝细胞性肝癌发生发展中的研究进展

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中文科技期刊数据库（全文版）医药卫生 2023年第6期 169-171页

作者：黄俊玲右江民族医学院附属医院广西百色533000

肝癌的原发性通常被认为是最危险的消化道癌,因其晚期预后非常糟糕。由于它的早期症状不明显,很易于被错误为另一种病变,并且目前的治疗方法也非常有限。incrna是指非编码的转录本,其大小通常超过200bp。最近的研究表明,incrna不仅参与... 详细信息

肝癌的原发性通常被认为是最危险的消化道癌,因其晚期预后非常糟糕。由于它的早期症状不明显,很易于被错误为另一种病变,并且目前的治疗方法也非常有限。incrna是指非编码的转录本,其大小通常超过200bp。最近的研究表明,incrna不仅参与了肝脏肿瘤的增长、扩散、上皮组织的变异、抗药物的作用、血管的形成和干细胞的分泌,而且还将作为一种重要的肿瘤标志物和治疗目标,从而开辟出一条全新的治疗途径。本文,从incrna的特点以及功能出发,阐述其在肝细胞性肝癌发生、进展中作用及研究进展,并探究特定incrna的检测及调控对肝细胞癌诊断和治疗的可行性。

关键词： incrna 肝细胞肝癌肿瘤标志物研究进展