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Transcriptome Survey of the Contribution of Alternative Splicing to Proteome Diversity in Arabidopsis thaliana

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Molecular Plant 2016年第5期9卷 749-752页

作者： haopeng yu Caihuan Tian Yang yu yuling Jiao State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences National Center for Plant Gene Research Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China The Middle School Attached to Beijing College of Petroleum Beijing 100083China

Dear Editor, Alternative splicing （AS） functions as a key regulatory mechanism and increases transcriptome and proteome diversity. Recent genome-wide studies have substantially expanded our estimation of the frequency of AS in plants （Reddy et al., 2013; Staiger and Brown, 2013）. However, the proportion of AS events that lead to increased proteome diversity in plants, rather than imperfect Dre-mRNA processing. remains unsolved. Here.

关键词： Survey Splicing Arabidopsis

Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells

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Science Bulletin 2017年第19期62卷 1304-1314页

作者： Yingying Han Xiao Chu haopeng yu Ying-Ke Ma Xiu-Jie Wang Wenfeng Qian yuling Jiao State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences University of Chinese Academy of Sciences Department of Biological Chemistry School of MedicineUniversity of California Key Laboratory of Genetic Network Biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences Beijing Institute of Genomics Chinese Academy of Sciences

Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.

关键词： Monoallelic gene expressionSingle-cell RNA-seqRice mesophyll cellsIndependent allelic expression

Comprehensive landscape of resistance mechanisms for neoadjuvant therapy in esophageal squamous cell carcinoma by single-cell transcriptomics

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Signal Transduction and Targeted Therapy 2023年第9期8卷 3920-3922页

作者： yushang Yang Yanguo Li haopeng yu Zhenyu Ding Longqi Chen Xiaoxi Zeng Shunmin He Qi Liao Yi Zhao Yong yuan Department of Thoracic Surgery West China HospitalSichuan UniversityChengduSichuanChina Zhejiang Key Laboratory of Pathophysiology Health Science CenterNingbo UniversityNingboZhejiangChina West China Biomedical Big Data Center West China HospitalSichuan UniversityChengduSichuanChina

Dear Editor,Preoperative neoadjuvant therapy combined with surgical resection is the standard treatment for locally advanced esopha-geal squamous cell carcinoma(ESCC).However,more than half of patients having a partial response to neoadjuvant therapy,which is considered as a therapy-resistant phenotype and the mechan-ism is still *** heterogeneity of the ESCC with surgery alone therapy were characterized by single-cell RNA sequencing(scRNA-seq)previously,but few report was about ESCC patients with neoadjuvant therapy.1 It is emergent to illustrate the comprehensive hallmarks of neoadjuvant therapy-resistance in ESCC at single cell level.

关键词： neoadjuvant squamous esophageal

OCT4 Condensates Play A Key Role in TAD Reorganization for Somatic Cell Reprogramming

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OCT4 Condensates Play A Key Role in TAD Reorganization for S...

RNA G-quadruplex structure contributes to cold adaptation in plants

2021年全国生物相分离和相变学术研讨会

作者： Jia Wang haopeng yu Qian Ma Junjun Ding Zhongshan School of Medicine Sun Yat-Sen University West China Hospital/West China School of Medicine Sichuan University

TADs may reorganize during cell fate ***,little is known about the mechanism by which TAD reorganization effects cell fate,as well as the master transcriptional regulator effects TAD ***,we demonstrate that TADs are reorganized during somatic cell reprogramming,which is correlated to gene regulation and cell fate ***,manipulation of TAD reorganization promotes ***,TAD reorganization is induced by the dynamics of concentrated chromatin loops in OCT4 phase-separated *** of OCT4 condensates attenuates TAD reorganization and reduces reprogramming efficiency,while rescue of the condensates restores TAD reorganization and enhances the ***,novel cell fate regulators can be identified by TAD reorganization-based Multiomics Analysis（TADMAN） in reprogramming and neural ***,our results elucidate the role and mechanism of TAD reorganization in cell fate transition.

关键词： TAD reorganization Master transcriptional regulator Condensate Phase separation Super-enhancer TADMAN

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RNA G-quadruplex structure contributes to cold adaptation in...

研究生学术规范养成教育存在的问题及对策研究

首届植物科学前沿学术大会

作者： Xiaofei Yang haopeng yu Huakun Zhang Yiliang Ding CAS Center for Excellence in Molecular Plant Sciences CAS-JIC Centre of Excellence for Plant and Microbial Science John Innes Centre Colney Lane Key Laboratory of Molecular Epigenetics of Ministry of Education Northeast Normal University

Nucleotide composition is suggested to infer gene functionality and ecological adaptation of species to distinct ***,the underlying biological function of nucleotide composition dictating environmental adaptations is largely *** this study,we systematically analyzed the nucleotide compositions of transcriptomes across 1000 plants(1 KP) and their corresponding ***,we found that plants growing in cold climates have guanine(G)-enriched transcriptomes,which are prone to forming RNA G-quadruplex *** immunofluorescence detection and in vivo structure profiling revealed that RNA G-quadruplex formation in plants was globally enhanced in response to ***-responsive RNA G-quadruplexes strongly enhanced mRNA stability,rather than affecting *** of individual RNA G-quadruplex promoted mRNA decay in the cold,leading to impaired plant cold ***,we propose that plants adopted RNA G-quadruplex structure as a molecular marker to facilitate their adaptation to the cold during evolution.

关键词： RNA G-quadruplex structure structure profiling cold temperature mRNA decay adaptation

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科技管理研究 2012年第11期32卷 222-225页

作者：喻浩朋河南师范大学外国语学院河南新乡453007

在当前国内学术界大环境下实施研究生学术规范养成教育存在不少困难。研究生群体对学术腐败现象认知有限、对自己恪守学术规范信心不足、知识产权意识淡薄,这些现象严重影响学术规范养成教育的实施。应充分意识到学术腐败对研究生学术... 详细信息

在当前国内学术界大环境下实施研究生学术规范养成教育存在不少困难。研究生群体对学术腐败现象认知有限、对自己恪守学术规范信心不足、知识产权意识淡薄,这些现象严重影响学术规范养成教育的实施。应充分意识到学术腐败对研究生学术规范养成教育的负面影响,采取多种措施加强学术规范养成教育的效果。

关键词：研究生学术规范养成问题与对策

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制图理论框架下汉语认识和真值情态动词研究

外国语 2019年第5期42卷 33-43页

作者：于浩鹏何晓炜河南师范大学外国语学院河南新乡453007 广东外语外贸大学英语语言文化学院广东广州510420

本文在制图理论框架下探讨汉语认识和真值情态动词语义特征和句法表现的映射关系。本研究发现汉语表达"可能性""盖然性"妁情态动词"可能"和"应该"既是认识情态(Epistemic Modal),也是真值情态(Alethic Modal)。根据制图理论(Cinque 1999... 详细信息

本文在制图理论框架下探讨汉语认识和真值情态动词语义特征和句法表现的映射关系。本研究发现汉语表达"可能性""盖然性"妁情态动词"可能"和"应该"既是认识情态(Epistemic Modal),也是真值情态(Alethic Modal)。根据制图理论(Cinque 1999,2006),前者位于标句词短语层,后者位于时制短语层。认识情态动词结构可分析为话题结构,句首名词是情态动词后接小句主语或宾语移位形成的话题。真值情态动词结构中的句首名词是位于时制短语指示语位置的主语。制图理论能够使我们更有效地探究情态动词语义特征与句法位置的映射关系。

关键词：制图理论认识情态真值情态句法语义

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汉语特殊型语言障碍儿童被动句理解研究

现代外语 2022年第1期45卷 53-65页

作者：于浩鹏杜娇何晓炜河南师范大学广东外语外贸大学英文学院广东省广州市510420

本文首次采用改良版句子图片匹配任务考察了平均年龄为5岁2个月(5;2)的汉语特殊型语言障碍(Specific Language Impairment,简称SLI)儿童被动句的理解状况。结果表明,汉语SLI儿童长被动句理解与短被动句相比存在更大困难;其长被动句理解... 详细信息

本文首次采用改良版句子图片匹配任务考察了平均年龄为5岁2个月(5;2)的汉语特殊型语言障碍(Specific Language Impairment,简称SLI)儿童被动句的理解状况。结果表明,汉语SLI儿童长被动句理解与短被动句相比存在更大困难;其长被动句理解能力与正常发展儿童相比存在缺陷,主要表现为论旨角色颠倒错误。根据边缘特征不明示假说,本文认为汉语SLI儿童长被动句理解困难是由其对该句式中移位名词的边缘特征不敏感而触发的相对近距效应造成的。与以往理论相比,边缘特征不明示假说更具有普遍意义,可统一解释英、汉SLI儿童被动句的理解损伤。

关键词：特殊型语言障碍被动句边缘特征不明示假说相对近距效应

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液-液相分离在细胞命运转变和疾病中的作用

四川大学学报:医学版 2023年第5期54卷 857-862页

作者：陈一龙凌晓茹于浩澎丁俊军四川大学医学大数据中心成都610041 四川大学华西医院生物医学大数据中心成都610041 四川大学“医学+信息”中心成都610041 中山大学中山医学院广州510080

液-液相分离作为一种细胞结构的组织与形成的新机制,在调控细胞命运转变和疾病发病机制中发挥着重要作用,正受到广泛关注。液-液相分离可形成一些具有液态流动性的细胞结构,如生殖颗粒、压力应激颗粒和核仁等经典的无膜细胞器,它们通常... 详细信息

液-液相分离作为一种细胞结构的组织与形成的新机制,在调控细胞命运转变和疾病发病机制中发挥着重要作用,正受到广泛关注。液-液相分离可形成一些具有液态流动性的细胞结构,如生殖颗粒、压力应激颗粒和核仁等经典的无膜细胞器,它们通常由生物大分子通过弱的多价相互作用形成的高浓度液体聚集而来。液-液相分离可参与调节细胞内的多种生命活动,其异常则会导致细胞功能紊乱,从而促进神经退行性疾病、传染病及癌症等疾病的发生发展。本综述通过总结各种无膜细胞器在生理与病理性细胞命运转变过程中的液-液相分离动态,揭示了它们在细胞分化、发育及各种疾病发生过程中的关键作用,为液-液相分离相关研究提供了新的理论框架和潜在的疾病治疗靶点,为未来的研究提供了新的方向。

关键词：相分离细胞命运转变疾病发病机制治疗策略综述