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Perspectives of DNA microarray and next-generation DNA sequencing technologies

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Science China(Life Sciences) 2009年第1期52卷 7-16页

作者： TENG XiaoKun1 & XIAO HuaSheng1,2.1 national Engineering center for Biochip at {2.,shanghai 2.12.3,China 2.{2.-MOST Key laboratory of health and disease genomics,chinese national human {12. center,shanghai 2.12.3,China national Engineering center for Biochip at {2. Shanghai 201203 China shanghai-MOST Key laboratory of {2. and disease genomics Chinese National Human Genome Center Shanghai 201203 China

DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of *** the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and *** next-generation DNA sequencing method was first introduced by the 454 Company in 2.03,immediately followed by the establishment of the Solexa and Solid techniques by other biotech *** it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray *** paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research.

关键词： DNA microarray next generation DNA sequencing genome

human genomics in China——Ten Years Endeavor:From Planning to Implementation

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Science China(Life Sciences) 2009年第1期52卷 2-6页

作者： CHEN Zhu and ZHAO Guo-Ping MOST-shanghai Key laboratory of {2. and health genomics The chinese national human genome center at shanghai The People’s Republic of China MOST-shanghai Key laboratory of {2. and health genomics The Chinese National Human Genome Center at Shanghai Shanghai The People’s Republic of China

Ten years ago, the chinese national human genome center at shanghai (South center,hereafter) was established in the Zhangjiang

关键词： Ten Years Endeavor human genomics in China

Identification and Characterization of glnA Promoter and its Corresponding Trans-regulatory Protein GlnR in the Rifamycin SV Producing Actinomycete,Amycolatopsis mediterranei U32

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Acta Biochimica et Biophysica Sinica 2006年第12期38卷 831-843页

作者： Hao YU~(1&) Wen-Tao PENG~1 Yang LIU~1 Ting WU~2.Yu-Feng YAO~1 Ming-Xue CUI~1 Wei-Hong JIANG~1 Guo-Ping ZHAO~(1,3,4*) 1 laboratory of Molecular Microbiology,Institute of Plant Physiology and Ecology,shanghai Institutes for Biological Sciences,{2. Academy of Sciences,shanghai 2.0032.China 2.Department of Medicinal Chemistry,School of Pharmacy,Fudan University,shanghai 2.0032.China 3 State Key laboratory of Genetic Engineering & Department of Microbiology,School of Life Science,Fudan University,shanghai 2.0433,China 4.laboratory of disease and health genomics,chinese national human genome center at shanghai,shanghai 2.12.3,China laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Department of Medicinal Chemistry School of Pharmacy Fudan University Shanghai 200032 China State Key laboratory of Genetic Engineering & Department of Microbiology School of Life Science Fudan University Shanghai 200433 China laboratory of disease and {2. genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

The genetic requirements for the transcription of glnA,encoding the major glutaminesynthetase in a rifamycin SV-producing Amycolatopsis mediterranei strain,U32.were *** experiments showed that the promoter of U32.glnA （pglnA） was likely to have two transcriptioninitiation sites:P1and P2.located 157 and 45 nucleotides （nt） upstream of the translational start codon,*** mobility shift and DNase I footprinting analyses revealed a 30 bp cis-element locatedat 45 to 75 nt downstream of P1,or 38 to 68 nt upstream of *** sequence of the cis-element displayedhigh similarity to the corresponding regions of pglnA from Streptomyces coelicolor and *** as a reporter gene,the expression levels of U32.pglnA and its deletion derivatives under differentnitrogen-source conditions were analyzed by detecting the catechol dioxygenase activities in ***54,*** J508 and *** FS10 （glnR mutant）.These in vivo studies showed that theactivation of U32.pglnA in *** required GlnR,and its binding to the U32.pglnA was furtherconfirmed by the gel mobility shift *** and heterologous expression of the U32.glnR allowed usto detect the in vitro interaction between the U32.GlnR and the corresponding pglnA *** shown by in vivo glnR inactivation and complementation indicated that GlnR is essential for theactive transcription of glnA in U32.

关键词： glnA promoter cis-element glnR Amycolatopsis mediterranei

Current research status of immunology in the genomic era

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Science China(Life Sciences) 2009年第1期52卷 43-49页

作者： LI HaoWen1,LI JinZhi1,ZHAO GuoPing2.& WANG Ying1,2.1 shanghai Institute of Immunology,Institute of Medical Science,shanghai Jiaotong University School of Medicine,shanghai 2.002.,China 2.shanghai-MOST Key laboratory of health and disease genomics,chinese national human genome {12.,shanghai 2.12.3,China 1. shanghai Institute of Immunology Institute of Medical Science Shanghai Jiaotong University School of Medicine Shanghai 200025 China 2. shanghai-MOST Key laboratory of {2. and disease genomics Chinese National Human Genome Center Shanghai 201203 China

This review updates the current status of immunology research under the influence of genomics,both conceptually and *** particularly highlights the advantages of employing the high-throughput and large-scale technology,the large genomic database,and bioinformatic power in the immunology *** fast development in the fields of basic immunology,clinical immunology(tumor and infectious immunology) and vaccine designing is illustrated with respect to the successful usage of genomic *** also speculate the future research directions of immunology in the era of genomics and post-genomics.

关键词： genomics immunology clinical immunology vaccine design

Current progress in epigenetic research for hepato-carcinomagenesis

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Science China(Life Sciences) 2009年第1期52卷 31-42页

作者： HUANG Jian national human {2. Research center at shanghai-Ministry of Science and Technology to build a healthy and disease Ge-nomics laboratory,shanghai 2.12.3,China 1. national human {2. Research center at shanghai-Ministry of Science and Technology to build a healthy and disease genomics laboratory Shanghai 201203 China

Hepatocellular carcinoma is the main type of primary liver cancer,and also one of the most malignant *** present,the pathogenesis mechanisms of liver cancer are not entirely *** has been shown that inactivation of tumor suppressor genes and activation of oncogenes play a significant role in carcinogenesis,caused by the genetic and epigenetic *** the past,people generally thought that genetic mutation is a key event of tumor pathogenesis,and somatic mutation of tumor suppressor genes is in particular closely associated with *** deeper understanding of tumors in recent years,increasing evidence has shown that epigenetic silencing of those genes,as a result of aberrant hypermethylation of CpG islands in promoters and histone modification,is essential to carcinogenesis and *** term epigenetics refers to heritable changes in gene expression caused by regulation mechanisms,other than changes in the underlying DNA *** epigenetic processes include DNA methylation,genome imprinting,chromotin remodeling,histone modification and microRNA *** paper reviews recent epigenetics research progress in the hepatocellular carcinoma study,and tries to depict the relationships between hepatocellular carcinomagenesis and DNA methylation as well as microRNA regulation.

关键词： tumor heaptocellular carcinoma epigenetics DNA methylation microRNA

Recent progress in 8igenomic research of liver cancer

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Science China(Life Sciences) 2009年第1期52卷 24-30页

作者： HAN ZeGuang shanghai-MOST Key laboratory for {2. and health genomics,chinese national human genome center at shanghai,shanghai 2.12.3,China 1. shanghai-MOST Key laboratory for {2. and health genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

Along the course of occurrence and development of liver cancer,the corresponding somatic cells accumulate some important genetic *** variations may be divided into two *** the genetic changes closely related to etiology of liver cancer,the well-known cases include insertion and integration of the hepatitis B virus(HBV) DNA after infection,and mutations at site 2.9 of the tumor suppressor gene p53 induced by exposure to aflatoxin *** secondary genetic changes include amplification and deletion of certain chromosome regions,mutations in p53 at the sites other than 2.9,as well as the mutational activation of the Wnt/β-catenin signal *** tumor cells with these genetic variations may gradually become the dominant clones under evolutionary ***,identification of genetic susceptible against risk of liver malignancy is also an important aspect of research in this field.

关键词： hepatocellular carcinoma chromosomal instability gene mutation oncogene tumor suppressor gene

Learn to fight from the war

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chinese Science Bulletin 2009年第13期54卷 2157-2158页

作者： ZHAO GuoPing shanghai-MOST Key laboratory for {2. and health genomics,chinese national human genome center at shanghai,shanghai 2.12.3,China Lab of Synthetic Biology,shanghai Institutes of Biological Sciences,chinese Academy of Sciences,shanghai 2.0031,China national Engineering Research center for Biochip Technology,shanghai Biochip Co.Ltd.,shanghai 2.12.3,China School of Life Sciences,Fudan University,shanghai 2.0433,China ZHONG Yang School of Life Sciences,Fudan University,shanghai 2.0433,China shanghai center for Bioinformation Technology,shanghai 2.02.5,China shanghai-MOST Key laboratory for {2. and health genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China Lab of Synthetic Biology Shanghai Institutes of Biological Sciences Chinese Academy of Sciences Shanghai 200031 China national Engineering Research center for Biochip Technology Shanghai Biochip Co. Ltd. Shanghai 201203 China School of Life Sciences Fudan University Shanghai 200433 China shanghai center for Bioinformation Technology Shanghai 200235 China

In March 2.09,a novel type A (H1N1) influenza broke out in North America and rapidly spread all over the world.

关键词：世界卫生组织战争军备竞赛 WHO 流感

Bacterial Type Ⅰ Glutamine Synthetase of the Rifamycin SV Producing Actinomycete,Amycolatopsis mediterranei U32.is the Only Enzyme Responsible for Glutamine Synthesis under Physiological Conditions

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Acta Biochimica et Biophysica Sinica 2006年第12期 821-830页

作者： Wen-Tao PENG~(1&) Jin WANG~1 Ting WU~2.Jian-Qiang HUANG~1 Jui-Shen CHIAO~1 Guo-Ping ZHAO~(1,3,4) 1 laboratory of Molecular Microbiology,Institute of Plant Physiology and Ecology,shanghai Institutes for Biological Sciences,{2. Academy of Sciences,shanghai 2.0032.China 2.Department of Medicinal Chemistry,School of Pharmacy,Fudan University,shanghai 2.0032.China 3 State Key laboratory of Genetic Engineering/Department of Microbiology,School of Life Science,Fudan University,shanghai 2.0433,China 4.laboratory of health and disease genomics,{2. {12. Haman genome center at shanghai,shanghai 2.12.3,China

The structural gene for glutamine synthetase,glnA,from Amycolatopsis mediterranei U32.wascloned via screening a genomic library using the analog gene from Streptomyces *** clone wasfunctionally verified by complementing for glutamine requirement of an Escherichia coli glnA null mutantunder the control of a lac *** analysis showed an open reading frame encoding a protein of466 amino acid *** deduced amino acid sequence bears significant homologies to other bacterialtype Ⅰ glutamine synthetases,specifically,71% and 72. identical to the enzymes of *** and Myco-bacterium tuberculosis,*** of this glnA gene in *** U32.led to glutamineauxotrophy with no detectable glutamine synthetase activity in *** contrast,the cloned glnA+gene cancomplement for both phenotypes in *** thus suggested that in *** U32.the glnA geneencoding glutamine synthetase is uniquely responsible for in vivo glutamine synthesis under our laboratorydefined physiological conditions.

关键词： glnA glutamine synthetase Amycolatopsis mediterranei rifamycin SV

Progress in the detection of human genome structural variations

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Science China(Life Sciences) 2009年第6期52卷 560-567页

作者： WU XueMei1,3 & XIAO HuaSheng1,2.1 center of Functional genomics,Key {2. of System Biology,shanghai Institutes for Biological Sciences,chinese Academy of Sciences,shanghai 2.0031,China 2.national Engineering center for Biochip at shanghai,shanghai 2.12.3,China 3 Graduate School of the chinese Academy of Sciences,shanghai 2.0031,China 1. center of Functional genomics Key Laboratory of System Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China 3. Graduate School of the chinese Academy of Sciences Shanghai 200031 China 2. national Engineering center for Biochip at {2. Shanghai 201203 China

The emerging of high-throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3 Mb in the human *** variants include copy number variations(CNVs),inversions,insertions,deletions and other complex rearrangements of DNA *** paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential ***,we highlight the array-based,PCR-based and sequencing-based assays,including array-based comparative genomic hybridization(aCGH),representational oligonucleotide microarray analysis(ROMA),multiplex amplifiable probe hybridization(MAPH),multiplex ligation-dependent probe amplification(MLPA),paired-end mapping(PEM),and next-generation DNA sequencing ***,we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.

关键词： structural variation cytogenetic microarray PCR paired end mapping(PEM) next-generation sequencing