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Exploring noncoding variants in genetic diseases:from detection to functional insights

Journal of Genetics and Genomics 2024年第2期51卷 111-132页

作者： Ke Wu Fengxiao Bu Yang Wu Gen Zhang Xin Wang shunmin he Mo-Fang Liu Runsheng Chen Huijun Yuan Institute of Rare Diseases West China Hospital of Sichuan UniversityChengduSichuan 610041China Key Laboratory of Systems health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiang 310024China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Molecular Biology State Key Laboratory of Cell BiologyShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China

Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.

关键词： Noncoding variation Genetic disease Research approach Challenge

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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

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SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 602-610页

作者： Yanyan Li Honghong Zhou Xiaomin Chen Yu Zheng Quan Kang Di Hao Lili Zhang Tingrui Song Huaxia Luo Yajing Hao Runsheng Chen Peng Zhang shunmin he College of Life Sciences University of Chinese Academy of Sciences.Beijing 100049China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of Sciences.Beijing 100101China University of Chinese Academy of Sciences.Beijing 100049 China Department of Cellular and Molecular Medicine University of California.San DiegoLa JollaCA 92093USA Guangdong Geneway Decoding Bio-Tech Co.Ltd Foshan 528316.China

Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome *** significance of small proteins has been revealed in current years,along with the discovery of their diverse ***,systematic annotation of small proteins is still *** Prot was specially developed to provide valuable information on small proteins for scientific *** we present the update of Sm Prot,which emphasizes reliability of translated s ORFs,genetic variants in translated s ORFs,disease-specific s ORF translation events or sequences,and remarkably increased data *** components such as non-ATG translation initiation,function,and new sources are also *** Prot incorporated638,958 unique small proteins curated from 3,165,229 primary records,which were computationally predicted from 419 ribosome profiling(Ribo-seq)datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species(Homo sapiens,Mus musculus,Rattus norvegicus,Drosophila melanogaster,Danio rerio,Saccharomyces cerevisiae,Caenorhabditis elegans,and Escherichia coli).In addition,small protein families identified from human microbiomes were also *** datasets in Sm Prot are free to access,and available for browse,search,and bulk downloads at http://***/SmProt/.

关键词： Ribosome profiling Small open reading frame Upstream open reading frame Variants Disease

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Identification and functional analysis of noval non coding RNAs in Xenopus

Identification and functional analysis of noval non coding R...

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生命的分子机器及其调控网络——2012年全国生物化学与分子生物学学术大会

作者： Xiumei Wang shunmin he Ying Liu Rongqiao he 中国科学院生物物理研究所中国科学院动物研究所

Noncoding RNAs(ncRNAs) are one of the major components of the brain ***,the roles of many ncRNAs are unclear,and the regulation of ncRNA expression is even much less *** analyzing more than 50 thousands of non-coding transcripts identified from the human fetal brain,high sequence conservation was found in the flank-ing 5’ or 3’ of the genomic loci of the *** applied the genome of Xenopus tropicalis to search for ncRNA candidates adjacent with the conserved genomic ***-fold ananlysis showed the similar second structure of ncRNAs in the brain of human fetus and xenopus and Xenc034 had a conserved sequence of tRNA and a stem-loop structure like *** the RT-PCR verification of four predicted ncRNAs

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Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia

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Journal of Genetics and Genomics 2021年第3期48卷 225-236页

作者： Jinhua Xiao Xianqin Wei Yi Zhou Zhaozhe Xin Yunheng Miao Hongxia Hou Jiaxing Li Dan Zhao Jing Liu Rui Chen Liming Niu Guangchang Ma Wenquan Zhen shunmin he Jianxia Wang Xunfan Wei Weihao Dou Zhuoxiao Sui Haikuan Zhang Shilai Xing Miao Shi Dawei Huang Institute of Entomology College of Life SciencesNankai UniversityTianjin 300071China Institute of Zoology Chinese Academy of SciencesBeijing 100101China Environment and Plant Protection Institute Chinese Academy of Tropical Agricultural SciencesHaikou 571101China Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation College of Marine SciencesBeibu Gulf UniversityQinzhou 535011China Institute of Biophysics Chinese Academy of SciencesBeijing 100101China Berry Genomics Corporation Beijing 102206China

Figs and fig pollinators are one of the few classic textbook examples of obligate pollination *** specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat ***,there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig *** fig syconia,there are also non-pollinator *** non-pollinator species differ in their evolutionary and life histories from *** conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published *** pollinators colonized the figs approximately 66.9 million years ago,consistent with the origin of host *** with nonpollinators,many more genes in pollinators were subject to relaxed *** genes were absent in pollinators in response to environmental stress and immune *** had more streamlined gene repertoires in the innate immune system,chemosensory toolbox,and detoxification *** results provide genomic evidence for the differentiation between pollinators and *** data suggest that owing to the long-term adaptation to the fig,some genes related to functions no longer required are absent in pollinators.

关键词： Phylogenetics Natural selection Immunity Chemosensory Adaptive evolution

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Study on Paleoearthquakes of the Eastern Liupanshan Piedmont Fault Zone

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Earthquake Research in China 1999年第4期13卷 69-77页

作者： Xiang Hongfa, Yasutaka Ikeda, Zhang Wanxia, Zhang Bingliang, Guo shunmin, and he HonglinInstitute of Geology, CSB, Beijing 100029, China Tokyo University, Tokyo 113, Japan

Based on trench excavation and detailed field investigation, the authors have ascertained that 6 paleoearthquake events have occurred in the Haizixia area of the Eastern Liupanshan Piedmont fault zone since 46Ka B.P. The recurrence time of 6 events were about 15000a, 20250a, 14750a, 12150a, 8550a and 4000a B.P., respectively, the recurrence intervals were about 15000a, 5500a, 2600a, 3600a and 4550a, respectively. According to M-D empirical relations, the vertical dislocation of events 1 and 2 corresponded to the dislocation of the earthquake with M8.0; the vertical dislocation of events 3-6, was corresponded to the dislocation of earthquakes with M6.5~7.5.

关键词： Paleoearthquake recurrence interval Liupanshan.

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“城市”的重启:改革开放初期报纸之上海

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都市文化研究 2019年第1期 26-41页

作者：何顺民淮阴师范学院复旦大学

本文以改革开放初期地方报纸积极介入的"上海病"、为"海派"正名、"洋奴"之辩的媒介讨论为经验材料,针对中国当前城市化进程中城市文化如何传承与创新的现实议题,返观历史,探讨抽象层面的城市文化精神与实体都市空间如何产生关联的问题... 详细信息

本文以改革开放初期地方报纸积极介入的"上海病"、为"海派"正名、"洋奴"之辩的媒介讨论为经验材料,针对中国当前城市化进程中城市文化如何传承与创新的现实议题,返观历史,探讨抽象层面的城市文化精神与实体都市空间如何产生关联的问题。本文认为,承载体制使命的地方大众媒介在特定时刻借由"上海病""海派文化""洋奴"之辩的讨论,"移动"了上海独特的历史文化讯息,重新连接历史和当下,长期隐伏于市民日常生活中的"空间"意识,通过上海历史、文化专家之口"隐隐约约"浮现,意味着"城市"的重新启动,并对后来的城市规划议题产生了深远的影响。

关键词：报纸城市空间意识海派洋味

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传播姿态的调适:《新闻联播》移动短视频的实践创新

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电视研究 2020年第9期 20-22页

作者：何顺民裴梦茹淮阴师范学院浙江传媒学院

为适应新的传播生态,中央广播电视总台《新闻联播》开启了移动短视频实践创新。新媒体产品《主播说联播》试图嵌入新的传播网络节点维持其社会地位,使国家主流价值的声音通过主持人个性化的表达得以在新传播网络中产生强大影响力。同时... 详细信息

为适应新的传播生态,中央广播电视总台《新闻联播》开启了移动短视频实践创新。新媒体产品《主播说联播》试图嵌入新的传播网络节点维持其社会地位,使国家主流价值的声音通过主持人个性化的表达得以在新传播网络中产生强大影响力。同时,因用户、媒介组织以及政策等多重因素的影响,约束着其传播姿态调适的界限和尺度。

关键词：《新闻联播》《主播说联播》短视频传播姿态

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制造“上海人”:都市共同体主体意识的苏醒——以20世纪90年代“上海人”媒介讨论为例

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城市学刊 2018年第5期39卷 81-87页

作者：何顺民淮阴师范学院传媒学院江苏淮安223300

20世纪90年代初上海处于再全球化的初始阶段,这时期几乎裹挟上海本地所有大众媒介对"上海人"的制造,成为全国一个独特的媒介现象。这场以"上海人"为话题的媒体话语运动跨越了不同社会阶层直至市民大众,形成了真正有意义的对话。上海地... 详细信息

20世纪90年代初上海处于再全球化的初始阶段,这时期几乎裹挟上海本地所有大众媒介对"上海人"的制造,成为全国一个独特的媒介现象。这场以"上海人"为话题的媒体话语运动跨越了不同社会阶层直至市民大众,形成了真正有意义的对话。上海地方媒介制造的"上海人"意味着上海城市共同体主体意识的初步苏醒。1990年代的上海人频频回首,试图寻找近代上海城市的历史文化资源,以兹借鉴而重建未来。

关键词：大众媒介上海人都市共同体主体意识

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“城市”的重启:改革开放初期报纸之上海

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新闻春秋 2019年第4期 75-84页

作者：何顺民淮阴师范学院

本文以改革开放初期地方报纸积极介入的'上海病'、为'海派'正名、'洋奴之辩'的媒介讨论为经验材料,针对中国当前城市化进程中城市文化如何传承与创新的现实议题,返观历史,探讨抽象层面的城市文化精神与实体城市空间的交往如何产生关联... 详细信息

本文以改革开放初期地方报纸积极介入的'上海病'、为'海派'正名、'洋奴之辩'的媒介讨论为经验材料,针对中国当前城市化进程中城市文化如何传承与创新的现实议题,返观历史,探讨抽象层面的城市文化精神与实体城市空间的交往如何产生关联的问题。本文认为,承载体制使命的地方大众媒介在特定时刻'移动'了上海独特的历史文化讯息,重新连接历史和当下,长期隐伏于市民日常生活中弥漫的'空间'意识,通过上海历史、文化专家之口'隐隐约约'浮现,意味着'城市'的重新启动,铭刻着城市的记忆。

关键词：报纸城市空间海派洋味

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