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Single-cell transcriptome analysis dissects lncrna-associated gene networks in Arabidopsis

Plant Communications 2024年第2期5卷 94-105页

作者： Zhaohui He Yangming Lan Xinkai Zhou Bianjiong Yu Tao Zhu Fa Yang Liang-Yu Fu Haoyu Chao Jiahao Wang Rong-Xu Feng Shimin Zuo Wenzhi Lan Chunli Chen Ming Chen Xue Zhao Keming Hu Dijun Chen State Key laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China Department of bioinformatics College of Life SciencesZhejiang UniversityHangzhou 310058China Jiangsu Key laboratory of Crop Genomics and Molecular Breeding/Key laboratory of Plant Functional Genomics of the Ministry of Education College of AgricultureYangzhou UniversityYangzhou 225009China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key laboratory of Crop Genetics and Physiology of Jiangsu Province Yangzhou UniversityYangzhou 225009China Zhejiang Zhoushan High School Zhoushan 316099China National Key laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops Hubei Hongshan LaboratoryWuhan 430070China

The plant genome produces an extremely large collection of long noncoding rnas(lncrnas)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological ***,we mapped the transcriptional heterogeneity of lncrnas and their associated gene reg-ulatory networks at single-cell *** generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell rna sequencing(scrna-seq)datasets from juvenile Arabidopsis *** then provided an in-depth analysis of cell-type-related lncrna signatures that show expression patterns consistent with canonical protein-coding gene *** further demon-strated that the cell-type-specific expression of lncrnas largely explains their tissue *** addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncrnas and mrnas,and we identified putative transcription factors orchestrating cell-type-specific expression of *** analysis results are available at the single-cell-based plant lncrna atlas data-base(scPLAD;https://***/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncrna biology and provides fundamental insights into lncrna expression specificity and associated gene regulation.

关键词： single-cell transcriptomics long noncoding rnas lncrnas gene regulatory networks GRNs plants

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Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes

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Medical Review 2022年第1期2卷 3-22页

作者： Zhaohui Qian Pei Li Xiaolu Tang Jian Lu Institute of Pathogen Biology Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China NHC Key laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100871China State Key laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100176China State Key laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China

The coronavirus disease 2019(COVID-19)pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public *** severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the causative agent of COVID-19,has evolved,thousands of single nucleotide variants(SNVs)have been identified across the viral *** roles of individual SNVs in the zoonotic origin,evolution,and transmission of SARS-CoV-2 have become the focus of many *** review summarizes recent comparative genomic analyses of SARS-CoV-2 and related coronaviruses(SC2r-CoVs)found in non-human animals,including delineation of SARS-CoV-2 lineages based on characteristic *** also discuss the current understanding of receptor-binding domain(RBD)evolution and characteristic mutations in variants of concern(VOCs)of SARS-CoV-2,as well as possible co-evolution between RBD and its receptor,angiotensin-converting enzyme 2(ACE2).We propose that the interplay between SARS-CoV-2 and host rna editing mechanisms might have partially resulted in the bias in nucleotide changes during SARS-CoV-2 ***,we outline some current challenges,including difficulty in deciphering the complicated relationship between viral pathogenicity and infectivity of different variants,and monitoring transmission of SARS-CoV-2 between humans and animals as the pandemic progresses.

关键词： molecular evolution population genetics severe acute respiratory syndrome coronavirus 2 variant virus.

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Identifying and annotating human bifunctional rnas reveals their versatile functions

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Science China(Life Sciences) 2016年第10期59卷 981-992页

作者： Geng Chen Juan Yang Jiwei Chen Yunjie Song Ruifang Cao Tieliu Shi Leming Shi Center for Pharmacogenomics School of Pharmacy and School of Life SciencesFudan UniversityShanghai 201203China The Center for bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China State Key laboratory of Genetic Engineering and MOE Key laboratory of Contemporary Anthropology School of Life SciencesFudan UniversityShanghai 201203China Fudan-Zhangjiang Center for Clinical Genomics Shanghai 201203China Zhanjiang Center for Translational Medicine Shanghai 201203China

Bifunctional rnas that possess both protein-coding and noncoding functional properties were less explored and poorly understood. Here we systematically explored the characteristics and functions of such human bifunctional rnas by integrating tandem mass spectrometry and rna-seq data. We first constructed a pipeline to identify and annotate bifunctional rnas,leading to the characterization of 132 high-confidence bifunctional rnas. Our analyses indicate that bifunctional rnas may be involved in human embryonic development and can be functional in diverse tissues. Moreover, bifunctional rnas could interact with multiple mirnas and rna-binding proteins to exert their corresponding roles. Bifunctional rnas may also function as competing endogenous rnas to regulate the expression of many genes by competing for common targeting mirnas. Finally,somatic mutations of diverse carcinomas may generate harmful effect on corresponding bifunctional rnas. Collectively,our study not only provides the pipeline for identifying and annotating bifunctional rnas but also reveals their important gene-regulatory functions.

关键词： bifunctional rna noncoding rna rna-seq tandem mass spectrometry

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rna Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells

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Genomics, Proteomics & bioinformatics 2023年第4期21卷 850-865页

作者： Boyang Shi Ke An Yueqin Wang Yuhan Fei Caixia Guo Qiangfeng Cliff Zhang Yun-Gui Yang Xin Tian Quancheng Kan Department of Pharmacy The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Henan Key laboratory of Precision Clinical Pharmacy Zhengzhou UniversityZhengzhou 450052China Key laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China MOE Key laboratory of bioinformatics Center for Synthetic and Systems BiologyBeijing Advanced Innovation Center for Structural BiologyTsinghua-Peking Joint Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China

Epidermal growth factor receptor-tyrosine kinase inhibitors(EGFR-TKIs)positively affect the initial control of non-small cell lung cancer(NSCLC).Rapidly acquired resistance to EGFR-TKIs is a major hurdle in successful ***,the mechanisms that control the resistance of EGFR-TKIs remain largely *** structures have widespread and crucial functions in many biological regulations;however,the functions of rna structures in regulating cancer drug resistance remain ***,the psoralen analysis of rna interactions and structures(PARIS)method is used to establish the higher-order rna structure maps of EGFRTKIs-resistant and-sensitive cells of *** results show that rna structural regions are enriched in untranslated regions(UTRs)and correlate with translation efficiency(TE).Moreover,yrdC N6-threonylcarbamoyltransferase domain containing(YRDC)promotes resistance to *** structure formation in YRDC 30 UTR suppresses embryonic lethal abnormal vision-like 1(ELAVL1)binding,leading to EGFR-TKI sensitivity by impairing YRDC translation.A potential therapeutic strategy for cancer treatment is provided using antisense oligonucleotide(ASO)to perturb the interaction between rna and *** study reveals an unprecedented mechanism through which the rna structure switch modulates EGFR-TKI resistance by controlling YRDC mrna translation in an ELAVL1-dependent manner.

关键词： rna structure EGFR-TKI resistance non-small cell lung cancer YRDC ELAVL1

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A novel tissue engineered nerve graft constructed with autologous vein and nerve microtissue repairs a longsegment sciatic nerve defect

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Neural Regeneration Research 2021年第1期16卷 143-149页

作者： Jing Wang Ya-Qiong Zhu Yu Wang Hong-Guang Xu Wen-Jing Xu Yue-Xiang Wang Xiao-Qing Cheng Qi Quan Yong-Qiang Hu Chang-Feng Lu Yan-Xu Zhao Wen Jiang Chen Liu Liang Xiao Wei Lu Chen Zhu Ai-Yuan Wang Spine Research Center of Wannan Medical College Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution(Wannan Medical College)Department of Spine SurgeryYijishan HospitalThe First Affiliated Hospital of Wannan Medical CollegeWuhuAnhui ProvinceChina Department of Ultrasound Chinese PLA General HospitalBeijingChina Department of Orthopedic Surgery Key Laboratory of Musculoskeletal Trauma&War Injuries PLABeijing Key Lab of Regenerative Medicine in OrthopedicsChinese PLA General HospitalBeijingChina Medical College of Nankai University TianjinChina The Neural Regeneration Co-Innovation Center of Jiangsu Province NantongJiangsu ProvinceChina Department of Anesthesiology the Second Affiliated Hospital of Inner Mongolia Medical UniversityHuhhotInner Mongolia Autonomous RegionChina Department of Orthopedic Surgery Yan’an University Affiliated HospitalYan’anShaanxi ProvinceChina Department of Orthopedic Surgery the First Affiliated Hospital of Medical CollegeShihezi UniversityShiheziXinjiang Uygur Autonomous RegionChina Department of Orthopedic Surgery The First Peoples’Hospital of Yunnan ProvinceKunmingYunnan ProvinceChina Department of Orthopedic Surgery Anhui Provincial HospitalThe First Affiliated Hospital of University of Science and Technology of ChinaHeifeiAnhui ProvinceChina

Veins are easy to obtain,have low immunogenicity,and induce a relatively weak inflammatory ***,veins have the potential to be used as conduits for nerve ***,because of the presence of venous valves and the great elasticity of the venous wall,the vein is not conducive to nerve *** this study,a novel tissue engineered nerve graft was constructed by combining normal dissected nerve microtissue with an autologous vein graft for repairing 10-mm peripheral nerve defects in *** with rats given the vein graft alone,rats given the tissue engineered nerve graft had an improved sciatic static index,and a higher amplitude and shorter latency of compound muscle action ***,rats implanted with the microtissue graft had a higher density and thickness of myelinated nerve fibers and reduced gastrocnemius muscle atrophy compared with rats implanted with the vein ***,the tissue engineered nerve graft had a lower ability to repair the defect than autogenous nerve *** summary,although the tissue engineered nerve graft constructed with autologous vein and nerve microtissue is not as effective as autologous nerve transplantation for repairing long-segment sciatic nerve defects,it may nonetheless have therapeutic potential for the clinical repair of long sciatic nerve *** study was approved by the Experimental Animal Ethics Committee of Chinese PLA General Hospital(approval No.2016-x9-07)on September 7,2016.

关键词： in vivo injury motor neurological function peripheral nerve injury rat recovery regeneration repair

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A Retrospective Analysis for Different Routes of Administration in Mice-Percutaneous Retro-Orbital, Jugular Catheter, Tail Vein and Femoral Cut Down Injections

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Journal of Biosciences and Medicines 2020年第9期8卷 131-141页

作者： Priyanka Prathipati Cristian Rodriguez-Aguayo Brian L Walton Anil K. Sood Jamieson Greaver Christopher F. Janssen Gabriel Lopez-Berestein Department of Advanced Cardiopulmonary Therapies and Transplantation Center for Advanced Heart Failure University of Texas Health Science Center at Houston Houston TX USA Department of Experimental Therapeutics University of Texas M.D. Anderson Cancer Center Houston TX USA The Center for rna Interference and non-coding rna University of Texas M.D. Anderson Cancer Center Houston TX USA Department of Cancer Biology University of Texas M.D. Anderson Cancer Center Houston TX USA Department of Gynecology Oncology & Reproductive Medicine University of Texas M.D. Anderson Cancer Center Houston TX USA Interdisciplinary Research Center for Laboratory Animal Medicine and Care University of Texas Health Science Center at Houston Houston TX USA

Liposomes effectively transport fatty proteins to targeted tissues. laboratory experiments use multiple methods to administer liposomes, but comparison of these methods is not available. In this retrospective study, we characterized and compared four intravenous administration routes (tail vein, jugular catheter, femoral vein and percutaneous retro-orbital injections) in murine models. ApoE-/- mice were used to compare administration routes. Results indicate that the jugular catheter route delivered the highest amount of liposomes to tissues due to longer period of injections compared to other routes;however, this route failed to remain patent for 8/10 animals. Delivery via tail vein, femoral vein and percutaneous retro-orbital injections resulted in similar accumulation in the organs. When including technical difficulty and expense, percutaneous retro-orbital injections of liposomes are the most convenient and efficacious approach.

关键词： Femoral Vein Jugular Catheter Liposomes Retro-Orbital Tail Vein

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rna2Immune:A Database of Experimentally Supported Data Linking non-coding rna Regulation to The Immune System

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Genomics, Proteomics & bioinformatics 2023年第2期21卷 283-291页

作者： Jianjian Wang Shuang Li Tianfeng Wang Si Xu Xu Wang Xiaotong Kong Xiaoyu Lu Huixue Zhang Lifang Li Meng Feng Shangwei Ning Lihua Wang Department of Neurology The Second Affiliated Hospital of Harbin Medical UniversityHarbin 150081China College of bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081China

non-coding rnas(ncrnas),such as micrornas(mirnas),long non-coding rnas(lncrnas),and circular rnas(circrnas),have emerged as important regulators of the immune system and are involved in the control of immune cell biology,disease pathogenesis,as well as vaccine responses.A repository of ncrna-immune associations will facilitate our understanding of ncrna-dependent mechanisms in the immune system and advance the development of therapeutics and prevention for immune ***,we describe a comprehensive database,rna2Immune,which aims to provide a high-quality resource of experimentally supported database linking ncrna regulatory mechanisms to immune cell function,immune disease,cancer immunology,and *** current version of rna2Immune documents 50,433 immune-ncrna associations in 42 host species,including(1)6690 ncrna associations with immune functions involving 31 immune cell types;(2)38,672 ncrna associations with 348 immune diseases;(3)4833 ncrna associations with cancer immunology;and(4)238 ncrna associations with vaccine responses involving 26 vaccine types targeting 22 ***2Immune provides a user-friendly interface for browsing,searching,and downloading ncrna-immune system ***,rna2Immune provides important information about how ncrnas influence immune cell function,how dysregulation of these ncrnas leads to pathological consequences(immune diseases and cancers),and how ncrnas affect immune responses to vaccines.

关键词： ncrna Immune cell Immune disease Cancer immunology Vaccine

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Sequence-Based Predicting Bacterial Essential ncrnas Algorithm by Machine Learning

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Intelligent Automation & Soft Computing 2023年第6期36卷 2731-2741页

作者： Yuan-nong Ye Ding-Fa Liang Abraham Alemayehu Labena Zhu Zeng bioinformatics and Biomedical Big data Mining laboratory Department of Medical InformaticsSchool of Big HealthGuizhou Medical UniversityGuiyang550025China Cells and Antibody Engineering Research Center of Guizhou Province Key Laboratory of Biology and Medical EngineeringSchool of Biology and EngineeringGuizhou Medical UniversityGuiyang550025China Key laboratory of Environmental Pollution Monitoring and Disease Control Ministry of EducationGuizhou Medical UniversityGuiyang550025China College of Computational and Natural Sciences Dilla UniversityDilla419Ethiopia

Essential ncrna is a type of ncrnawhich is indispensable for the sur-vival of *** essential ncrnas cannot encode proteins,they are as important as essential coding genes in *** have got wide variety of applications such as antimicrobial target discovery,minimal genome construction and evolution *** present,the number of species required for the deter-mination of essential ncrnas in the whole genome scale is still very few due to the traditional methods are time-consuming,laborious and *** addition,tra-ditional experimental methods are limited by the organisms as less than 1%of bacteria can be cultured in the ***,it is important and necessary to develop theories and methods for the recognition of essential non-coding *** this paper,we present a novel method for predicting essential ncrna by using both compositional and derivative features calculated by information theory of ncrna *** method was developed with Support Vector Machine(SVM).The accuracy of the method was evaluated through cross-species cross-vali-dation and found to be between 0.69 and *** shows that the features we selected have good performance for the prediction of essential ncrna using ***,the method can be applied for discovering essential ncrnas in bacteria.

关键词： bioinformatics biological information theory biomedical informatics

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PlantcircBase： A Database for Plant Circular rnas

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Molecular Plant 2017年第8期10卷 1126-1128页

作者： Qinjie Chu Xingchen Zhang Xintian Zhu Chen Liu Lingfeng Mao Chuyu Ye Qian-Hao Zhu Longjiang Fan Institute of Crop Science and Institute of bioinformatics Zhejiang University Hangzhou 310058 China CSIRO Agriculture and Food Canberra ACT 2601 Australia

Dear Editor Circular rnas （circrnas） are a kind of non-coding rnas; they were first found over 35 years ago but have only become a research hotspot in recent years. Circrnas are covalently closed loops derived from precursor mrnas by non-sequential back-splicing. Based on their genomic location, circrnas can be classified into exonic, intronic, intergenic, and exon-intronic circrnas （Chen, 2016）. By taking advantages of recent advances in bioinformatics algorithms, a large number of circrnas have been detected among diverse organisms,

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Global signatures of protein binding on structured rnas in Saccharomyces cerevisiae

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Science China(Life Sciences) 2014年第1期57卷 22-35页

作者： YANG YuCheng UMETSU Jumpei LU Zhi John MOE Key Lab of bioinformatics School of Life Sciences Tsinghua University Department of Biological Information Tokyo Institute of TechnologyTokyo 152-8850 Japan

Protein binding is essential to the transport,decay and regulation of almost all rna ***,the structural preference of protein binding on rnas and their cellular functions and dynamics upon changing environmental conditions are poorly ***,we integrated various high-throughput data and introduced a computational framework to describe the global interactions between rna binding proteins(RBPs)and structured rnas in yeast at single-nucleotide *** found that on average,in terms of percent total lengths,~15%of mrna untranslated regions(UTRs),~37%of canonical non-coding rnas(ncrnas)and^11%of long ncrnas(lncrnas)are bound by *** RBP binding sites,in general,tend to occur at single-stranded loops,with evolutionarily conserved signatures,and often facilitate a specific rna structure conformation in *** found that four nucleotide modifications of trna are significantly associated with RBP *** also identified various structural motifs bound by RBPs in the UTRs of mrnas,associated with localization,degradation and stress ***,we identified>200 novel lncrnas bound by RBPs,and about half of them contain conserved secondary *** present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome,emphasizing their structural context and cellular functions.

关键词： rna binding protein non-coding rna UTR rna structure Saccharomyces cerevisiae

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