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Acidic domains differentially read histone H3 lysine 4 methylation status and are widely present in chromatin-associated proteins

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中国科学：生命科学英文版 2017年第2期60卷 138-151页

作者： Meng Wu Wei Wei Jiwei Chen Rong Cong tieliu shi Jiwen Li Jiemin Wong James X.Du Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Collaborative Innovation Center for Cancer Medicine Sun Yat-Sen University Cancer CenterGuangzhou 510060China University de Lyon Ecole Normale Supdrieure de LyonCNRS USR 3010Laboratoire Joliot-CurieLyon 69364France

Histone methylation is believed to provide binding sites for specific reader proteins, which translate histone code into biological function. Here we show that a family of acidic domain-containing proteins including nucleophosmin (NPM1), pp32, SET/TAF1β, nucleolin (NCL) and upstream binding factor (UBF) are novel H3K4me2-binding proteins. These proteins exhibit a unique pattern of interaction with methylated H3K4, as their binding is stimulated by H3K4me2 and inhibited by H3K4me1 and H3K4me3. These proteins contain one or more acidic domains consisting mainly of aspartic and/or glutamic residues that are necessary for preferential binding of H3K4me2. Furthermore, we demonstrate that the acidic domain with sufficient length alone is capable of binding H3K4me2 in vitro and in vivo. NPM1, NCL and UBF require their acidic domains for association with and transcriptional activation of rDNA genes. Interestingly, by defining acidic domain as a sequence with at least 20 acidic residues in 50 continuous amino acids, we identified 655 acidic domain-containing protein coding genes in the human genome and Gene Ontology (GO) analysis showed that many of the acidic domain proteins have chromatin-related functions. Our data suggest that acidic domain is a novel histone binding motif that can differentially read the status of H3K4 methylation and is broadly present in chromatin-associated proteins.

关键词：组蛋白H3 相关蛋白甲基化染色质酸性赖氨酸状态阅读

QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

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Science China(Life Sciences) 2019年第7期62卷 937-946页

作者： Xiangjun Ji Weida Tong Baitang Ning Christopher E. Mason David P. Kreil Pawel P. Labaj Geng Chen tieliu shi The Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China National Center for Toxicological Research U.S. Food and Drug Administration3900 NCTR RDJefferson AR 72079USA Department of Physiology and Biophysics Weill Cornell MedicineNew York 10065USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine New York 10021USA Feil Family Brain & Mind Research Institute New York 10065USA Chair of Bioinformatics Research Group Boku UniversityVienna A-1190Austria Malopolska Centre of Biotechnology Jagiellonian UniversityKrakow 30-387Poland APART Fellow Austrian Academy of ScienceVienna A-1190Austria National Center for International Research of Biological Targeting Diagnosis and Therapy Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy ResearchCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNanning 530021China

RNA sequencing(RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse ***,transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing ***,we introduce an efficient tool,QuaPra(Quadratic Programming combined with Apriori),for accurate transcriptome assembly and *** could detect at least 26.5% more low abundance(0.1–1 FPKM) transcripts with over 2.7% increase of sensitivity and precision on simulated data compared to other currently popular ***,around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing *** is freely available at http://***/QuaPra/.

关键词： RNA-Seq transcriptome reconstruction transcript assembly transcript quantification

Comparative analysis of whole-genome sequences of Streptococcus suis

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Chinese Science Bulletin 2006年第10期51卷 1199-1209页

作者： WEI Wu DING Guohui WANG Xiaojing SUN dingchun TU Kang HAO Pei WANG Chuan CAO Zhiwei shi tieliu LI Yixue Bioinformation Center Shanghai Institutes for Biological Sciences/Graduate School of the Chinese Academy of Sciences Shanghai 200031 China Shanghai Center for Bioinformation Technology Shanghai 200235 China

The outbreak of Streptococcus suis re-cently in some districts of Sichuan Province in China has caused over 30 deaths and over 200 infections in human beings. In order to study the pathogenicity mechanism and to prevent the bacteria from spreading and infecting human beings and swine, we have annotated and analyzed the genomes of two strains, Streptococcus suis P1/7 and 89-1591 re-spective1y. The whole length of P1/7 is 2.007 Mb, and has 1969 ORFs. In contrast, the partial genome sequence of 89-1591 is 1.98 Mb in length and exists in 177 contigs with 1918 ORFs. Analysis shows that the average lengths of CDSs in two genomes are very close, and the numbers of the homolog ORFs are 1306 between those two strains. Most of the tox-icity factors of the two strains are homologeous, but there are still some significant differences between those two strains. For example, among the 11 genes (cps2A―cps2K) encoding for the capsules in P1/7, 4 (cps2A, 2B, 2I, 2J) are not detected in strain 89-1591. At the same time, the genes encoding EF and Haemolysin in P1/7 are also not found in strain 89-1591. Besides, the genes related to DNA replica-tion, repair and recombination differ from each other significantly and there also exist certain differences among the surface proteins. Those characteristics indicate that those two strains have evolved their ownspecific functions to adapt to the different environ-ments and that the pathogenesis of the two strains is different. We have accumulated comprehensive ge-nomics information for future systematic studies of S. sui. Our results are helpful for disease prevention, vaccine development, as well as drug design for S. suis.

关键词：链球菌 P1/7菌株 89-1591菌株比较分析基因序列分析

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新技术能使DNA测序的成本降低多少?

科学通报 2017年第19期62卷 2042-2046页

作者：石铁流华东师范大学生命科学学院上海市调控生物学重点实验室生物信息学及计算生物学中心上海200241

1977年,Sanger及其同事发明出最早的DNA测序技术,1990年开始的人类基因组计划催生了DNA测序技术的自动化.近10多年来,新一代测序技术得到了飞速的发展,测序速度及测序通量的巨大提升使得个人基因组的测序成本急剧下降,达到了1000美元一... 详细信息

1977年,Sanger及其同事发明出最早的DNA测序技术,1990年开始的人类基因组计划催生了DNA测序技术的自动化.近10多年来,新一代测序技术得到了飞速的发展,测序速度及测序通量的巨大提升使得个人基因组的测序成本急剧下降,达到了1000美元一个全基因组的水平,从而使得DNA测序技术在生命科学研究领域以及临床医学上有着更广阔的应用前景.近来出现的第三代测序技术具有测序过程中无需PCR扩增而且产生非常长的测序片段的优势.尽管其测序的准确性只达到85%左右且成本高,但仍然显示出了较好的前景."精准医学"时代的来临将进一步促进DNA测序技术的革新,并使个人基因组测序成本进一步下降,有望使个人基因组测序成本进入百美元的时代.随着海量的测序数据的积累,如何有效地分析和解读这些测序数据面临着巨大的挑战,生物信息学在此过程中扮演着关键的角色.

关键词： DNA测序技术个人基因组测序成本新一代测序技术第三代测序技术

Interplay of transcription factors and microRNAs during embryonic hematopoiesis

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Science China(Life Sciences) 2017年第2期60卷 168-177页

作者： Xueping Gong Ruihua Chao Pengxiang Wang Xiaoli Huang Jingjing Zhang Xiaozhou Zhu Yanyang Zhang Xue Yang Chao Hou Xiangjun Ji tieliu shi Yuan Wang Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai 200241 China

Hematopoietic stem cells (HSCs), which are localized in the bone marrow of adult mammals, come from hematopoietic endothelium during embryonic stages. Although the basic processes of HSC generation and differentiation have been described in the past, the epigenetic regulation of embryonic hematopoiesis remains to be fully described. Here, by utilizing an in vitro differentiation system of mouse embryonic stem cells (ESCs), we identified more than 20 microRNAs that were highly enriched in embryonic hematopoietic cells, including some (e.g. miR-10b, miR-15b, and miR-27a) with previously unknown functions in blood formation. Luciferase and gene expression assays further revealed combinational binding and regulation of these microRNAs by key transcription factors in blood cells. Finally, bioinformatics and functional analyses supported an interactive regulatory control between transcription factors and microRNAs in hematopoiesis.

关键词： microRNA 造血干细胞转录因子胚胎期相互作用小鼠胚胎干细胞遗传调控成年哺乳动物

Application of genome analysis strategies in the clinical testing for pediatric diseases

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Pediatric Investigation 2018年第2期2卷 72-81页

作者： Yaqiong Jin Li Zhang Baitang Ning Huixiao Hong Wenming Xiao Weida Tong Yiran Tao Xin Ni tieliu shi Yongli Guo Beijing Key Laboratory for Pediatric Diseases of Otolaryngology Head and Neck Surgery MOE Key Laboratory of Major Diseases in Children Beijing Pediatric Research Institute Beijing Children's Hospital Capital Medical University National Center for Children's Health Beijing China Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai China National Center for Toxicological Research U.S.Food and Drug Administration Jefferson AR USA

Next-generation sequencing (NGS) is being used in clinical *** authorities in both China and the United States are overseeing the clinical application of NGS instruments and *** addition,the US Association for Molecular Pathology and the College of American Pathologists have jointly released a guidance to standardize the analysis and interpretation of NGS data involved in clinical *** present,the analysis strategies and pipelines for NGS data related to the clinical detection of pediatric disease are similar to those used for adult ***,for rare pediatric diseases without linkage to known genetic variants,it is currently difficult to detect the relevant pathogenic genes using NGS ***,it is challenging to identify novel pathogenic genes of familial pediatric ***,characterization of the pathogenic genes associated with above diseases is important for the diagnosis and treatment of rare diseases in *** article introduces the general pipelines for NGS data analyses of diseases and elucidates data analysis strategies for the pathogenic genes of rare pediatric diseases and familial pediatric tumors.

关键词： Familial pediatric tumors Next-generation sequencing Rare pediatric diseases

Disease spectrum analysis of hospitalized children in China: A study of 18 tertiary children's hospitals

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Pediatric Investigation 2019年第3期3卷 159-164页

作者： Guoshuang Feng Yueping Zeng Jian Tian Xinyu Wang Jun Tai Fei Song Xin Zhang Xin Xu Jun Chen tieliu shi Xin Ni Big Data and Engineering Research Center Beijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijingChina Beijing Advanced Innovation Center for Big Data-Based Precision Medicine Beihang University&Capital Medical UniversityBeijingChina Medical Record Management Office Beijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijingChina Hospital Administration Office Beijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijingChina Department of Otolaryngology Head and Surgery Beijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijingChina Department of Scientific Research Beijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijingChina Information Center Beijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijingChina The Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEastChina Normal UniversityShanghaiChina

Importance: Morbidity and mortality of children are important indicators of the performance of the public health system in any country. In China, the children's disease spectrum has gradually changed in recent years. However, the gender- and age-specific disease spectrum for hospitalized children under 15 years old is still unclear. Objective: To explore the gender- and age-based distribution of diseases in hospitalized children under 15 years in China. Methods: Medical records home page data for 2016 to 2018 were collected from 18 tertiary children's hospitals in China. The gender- and age-specific disease spectrum was analyzed, using the tenth revision of the International Statistical Classification of Diseases and Related Health Problems (ICD-10). Results: The most common diseases were those of the respiratory system (25.7% of all 2232142 hospitalized children). The top three diseases for boys were diseases of the respiratory system (25.6%), diseases of the digestive system (11.4%) and certain conditions originating in the perinatal period (8.6%). The top three diseases for girls were diseases of the respiratory system (25.9%), certain conditions originating in the perinatal period (10.1%), and factors influencing health status and contact with health services (9.4%).The most common diseases for children under 1 year old were certain conditions originating in the perinatal period (38.1%). For all other age groups, the most common conditions were respiratory diseases (33.8% for those aged 1–3 years, 25.2% for those aged 4–6 years, and 12.2% for those aged 7–14 years). Interpretation: This study analyzed the medical records home pages of 18 children's hospitals to provide the first overview of the disease spectrum and its gender- and age-specific distribution among children in China.

关键词： Disease spectrum Hospitalized children China

TCMID 2.0:a comprehensive resource for TCM

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TCMID 2.0:a comprehensive resource for TCM

Comprehensive identification and function study of Arabidopsis chloroplast proteome through systems biology approaches

“农业健康与环境”组学大数据整合生物信息学研讨会

作者： Lin Huang Yan shi Yiran Yu Duoli Xie Huanlong Liu tieliu shi Chengping Wen TCM Clinical Basis Institute Zhejiang Chinese Medicine University Center for Bioinformatics and Computational Biology and The Institute of Biomedical SciencesCollege of Life ScienceEast China Normal University

As a traditional medical intervention in Asia and a complementary and alternative medicine in western countries,Traditional Chinese Medicine(TCM) is capturing worldwide attention in life science *** Chinese Medicine Integrated Database(TCMID),which was originally launched in 2013,was a comprehensive database aiming at TCM’s modernization and *** has been highly recognized among pharmacologists and scholars in TCM *** latest release,TCMID 2.0(http://***/tcmid/),replenished the preceding database with 18,203 herbal ingredients,15 prescriptions,82 related targets,1,354 drugs,1,572 diseases and numerous new connections between *** that chemical changes might take place in decocting process of prescriptions,which may result in new ingredients,new data containing the prescription ingredients was collected in current *** addition,778 herbal mass spectrometry(MS) spectra related to 170 herbs were appended to show the variation of herbal quality in different origin and distinguish genuine medicinal materials from common ones while 3,895 MS spectra of 729 ingredients were added as the supplementary materials of component *** the significant increase of data,TCMID 2.0 will further facilitate TCM’s modernization and enhance the exploration of underlying biological processes that are response to the diverse pharmacologic actions of TCM.

关键词： Traditional Chinese Medicine(TCM) database mass spectrometry network

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Comprehensive identification and function study of Arabidops...