人类基因组研究进展及其产业化前景

人类基因组研究关系到人类生存与健康的各个方面 ,成为医药生物技术产业创新的重要源头 ,将产生巨大的社会效益和经济效益。 2 0世纪末启动的人类基因组计划被公认为是生命科学发展史上的里程碑 ,随着人类基因组、水稻基因组、拟南芥基因组及其它重要微生物等 5 0多种生物基因组全序列测定工作的完成 ,目前国际基因组研究开发的总体趋势已发生了变化 ,功能基因组研究成为竞争的焦点。我国在人类基因组研究方面已取得令人瞩目的成绩 ,如在世界上首次克隆了人神经性高频耳聋、遗传性乳光牙等一批疾病基因 ,收集、保存了一批宝贵的遗传资源 ,建立了国家级的、在国际上具有初步竞争实力的人类基因组研究基地等。综述了近年来人类基因组研究、开发现状及我国在该领域所具备的一些工作基础 ,并对加速我国人类基因组研究提出了一些建议。     

微生物蛋白质组学研究进展

微生物基因组研究作为人类基因组计划的一部分 ,对人类基因组计划及微生物学 ,甚至整个生命科学都产生巨大的影响[1] 。人类基因组测序已经取得突破性进展 ,现已绘制完毕人类基因组的工作草图 ,人类基因组计划即将提前完成。目前已采用ＤＮＡ ＲＮＡ芯片和基因表达序列分析 (ｓｅｒｉａｌａｎａｌｙｓｉｓｏｆｇｅｎｅｅｘｐｒｅｓｓｉｏｎ ,ＳＡＧＥ)来研究基因组的功能[2 ,3 ] 。但随着对基因组研究的深入 ,人们认识到单纯从基因组信息并不可能完全揭示生命的奥秘。因为蛋白质是生物功能的体现者 ,这使我们不得不考虑基因编码的蛋白质有什…     

TILLING在水稻育种中的应用前景

TILLING(Targeting Induced Local Lesions in Genomes)是功能基因组研究中应用的一种反向遗传学技术。它能高通量低成本地在EMS诱变群体中鉴定出发生在特定基因上的点突变。在其基础上发展出的EcoTILLING技术则可发现种质资源中的SNP位点及小插入或缺失多态性位点。水稻是非常重要的粮食作物, 也是已经完成了全基因组序列测定,有丰富的生物信息学资源可以利用的基因组研究模式植物。水稻的分子标记辅助育种将在育种中扮演越来越重要的角色。在这样的背景下,本文从基于特定基因的种质资源鉴定、EMS诱变育种、及水稻功能标记开发等方面论述了其在水稻育种中的应用前景。     

CRISPR/Cas9全基因组筛选在生命科学中的应用

全基因组筛选是系统性分析基因组的有力工具,可在全基因组范围内发现具有特定生物学功能的基因或DNA元件。基于CRISPR/Cas9基因编辑技术的全基因组筛选具有高通量和高效率的特点,已被广泛应用于疾病机理和药物开发等研究,为临床治疗提供科学用药依据。同时,CRISPR/Cas9筛选可靶向启动子、增强子和长链非编码RNA等序列,解析其调控基因表达的功能。此外,将全基因组筛选与单细胞测序技术结合,可揭示细胞转录组差异,剖析基因功能关系。     

基因表达系列分析法(SAGE)的改进及其在植物功能基因组研究中的应用

基因表达系列分析方法(SAGE)是一种新的基因表达分析方法,与基因芯片技术一样具有高通量的特点,可测定特定组织的基因表达水平,在全基因组水平上同时定量检测数万个基因表达模式;可在未知目的基因的前提下,分析来自一个细胞的全部转录本信息;对已知或未知基因表达进行定性和定量分析.目前,虽然在疾病、发育、细胞凋亡、药物筛选等多个领域已有利用SAGE方法进行的研究,但该方法在植物功能基因组研究中的应用相对较少.本文主要综述了该方法在RNA用量、PCR循环次数、SAGE效能和可靠性、标签长度和未知标签分析等方面的改进及其在植物中构建SAGE文库、筛选新基因、基因表达图谱分析等方面的应用,从而为其在植物功能基因组研究中的进一步应用提供理论参考.     

基于CRISPR/Cas9系统高通量筛选研究功能基因

利用功能缺失型(Loss-of-function)或者功能获得型(Gain-of-function) 策略高通量筛选功能基因,是研究人员快速寻找调控特定表型的重要或关键基因的主要方法。RNA干扰(RNA interference,RNAi)的遗传筛选方法因操作简单、成本相对较低等优势,尽管已经得到了广泛的应用,然而其抑制效果不完全、脱靶效应明显等劣势依然存在。近年来兴起的CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeat sequences/ CRISPR-associated protein 9)技术能快速、简便、准确地实现基因组敲除等编辑功能,因而成为一种强大的遗传筛选工具;在各种细胞系、人和小鼠及斑马鱼等多种模式动物中,大规模运用该方法筛选功能基因已经取得了巨大成功。本文总结了CRISPR/Cas9技术的特点,将其与传统基因工程方法进行了分析比较,回顾了近期相关的高通量功能基因筛选工作,最后探讨了该技术未来的发展趋势。     

植物功能基因组研究进展

随着植物基因组计划的深入,植物基因组学研究的重点已经转变为基因组功能的研究,即利用基因组序列的信息和高通量的系统分析技术,在基因组水平研究植物结构和组织与植物功能在细胞、有机体和进化上的关系.对功能基因组学研究的内容、方法以及最新研究进展进行了综述.     

基于cDNA测序与杂交的大规模基因组分析方法

随着人类及其他多种模式生物基因组计划所取得的重大进展 ,目前 ,基因组研究正处于一个从“序列基因组”研究向“功能基因组”研究的重大转折时期。诚然 ,通过“序列基因组”研究可以了解到大量的有关组成基因组所有核苷酸排列顺序的信息 ,但是 ,我们对由这些核苷酸所组成的基因的功能及这些基因的时空表达顺序却知之甚少。比如 ,通过人类基因组计划可以知道组成人类基因组的大约 3 0亿个核苷酸在染色体上是如何排列的 ,而由这些核苷酸可构成哪些基因 ?这些基因具有何种功能 ?这些基因在不同的组织、不同的发育阶段又是如何表达的 ?这正是“…     

DNA微阵列技术及其在肿瘤生物学中的应用

人类基因组测序工作的完成使人们可以方便地调用任何基因序列,但仅有基因序列并不能解释众多的生物学问题,这要求发展一种高通量的技术用于研究基因的生物学功能以及基因的相互作用。DNA微阵列技术以其高通量的特点,已经在肿瘤生物学的研究中逐渐被采用。由于癌症是源于基因表达谱改变的基因疾病,通过DNA微阵列技术研究癌症细胞和对应的正常细胞的基因表达差异,将会使人们更好地了解肿瘤的形成和发展过程。     

目标序列捕获技术及其应用

耗资30 亿美元历时10 余年完成的人类基因组计划(Human Genome Project,HGP)给基因组学研究带来了翻天覆地的变化,通过测定人类基因组DNA 的序列,探寻基因在染色体上的位置,明确基因的结构和功能,解读人类的全部遗传信息,人类第一次在分子水平上全面认识自我.在这期间,建立了两项非常重要的高通量技术:基因芯片和新一代测序技术.这两种技术进一步结合,就产生了一种新的解决方案:目标序列捕获测序技术.新一代测序技术的发展和成功应用使得普通实验室对整个人类基因组进行测序成为可能,由此,科学家们提出了千元人类基因组计划①.     

TILLING技术在功能基因组学中的应用

TILLING(定向诱导基因组局部突变)技术是近年发展起来的一种高通量筛选化学诱变的点突变的技术,它利用专一识别点突变的核酸酶结合PCR来检测单核苷酸多态性(SNP)。TILLING技术起源于植物基因组研究,逐渐扩展到动物及人类功能基因组学的研究中。无论是筛选突变体还是研究特定基因的重要性,TILLING都具有高通量、自动化的优势。随着此项技术应用范围的扩展,从诱变剂和内切酶的选择到具体的操作方式,以及结果的识别和统计方法,都有了不少改进。在其他相关学科不断发展的大环境下,TILLING技术也在不断发展,其在功能基因组学研究中的作用也会更显著。     

Approaches to lipid metabolism gene identification and characterization in the postgenomic era

The availability of genomic resources has already had a tremendous impact on biomedical research. In this review, we describe how whole genome sequence and high-throughput functional genomics projects have facilitated the identification and characterization of important genes in lipid metabolism and disease. We review key approaches and lipid genes identified in the first years of this century and discuss how genomic resources are likely to streamline gene identification and functional characterization in the future.     

Advances in genomics for microbial food fermentations and safety

The exponentially growing collection of genomic sequence information, the high-throughput analysis of expression products, and the ability to order this information using advanced bioinformatics are expected to affect biotechnology and life sciences in a profound and unprecedented way. These developments offer many possibilities to improve the functionality of fermentations by food-grade microorganisms and to increase the microbial safety of foods. It will be necessary to combine functional studies with comparative genomics approaches to provide effective strategies for improving the functionality and safety of foods.     

Status of genome projects for nonpathogenic bacteria and archaea

Since the first microbial genome was sequenced in 1995, 30 others have been completed and an additional 99 are known to be in progress. Although the early emphasis of microbial genomics was on human pathogens for obvious reasons, a significant number of sequencing projects have focused on nonpathogenic organisms, beginning with the release of the complete genome sequence of the archaeon Methanococcus jannaschii in 1996. The past 18 months have seen the completion of the genomes of several unusual organisms, including Thermotoga maritima, whose genome reveals extensive potential lateral transfer with archaea; Deinococcus radiodurans, the most radiation-resistant microorganism known; and Aeropyrum pernix, the first Crenarchaeota to be completely sequenced. Although the functional characterization of genomic data is still in its initial stages, it is likely that microbial genomics will have a significant impact on environmental, food, and industrial biotechnology as well as on genomic medicine.     

环境微生物不依赖于培养的基因组学研究及应用

微生物在生物圈中分布广泛,并且在地球物质循环中占有重要地位,但是约99﹪的微生物目前还不能通过传统的培养方法得到纯培养物（即未培养微生物）,给这些未培养微生物的研究带来很大的困难。随着分子生物学的快速发展及其在微生物研究中的广泛运用,促进了以环境中未培养微生物为研究对象的新兴学科--环境基因组学的产生和发展。在不进行相关微生物培养分离的情况下,通过从环境样品中直接提取获得所有微小生物的全部遗传物质,并构建环境基因组文库;进一步利用功能基因组学研究策略,从文库中寻找编码产生新的有生物活性产物的基因;通过对系统发育相关锚定位点基因序列分析,从而确定特定生态环境体系中未培养微生物的种类结构组成及进化地位,并最终重建该体系中微生物群体的基本物质循环模式。此外,环境基因组学也可以在对未培养微生物生理生化特性深入了解的基础上,建立发展合适的培养体系,最终获得某些特定微生物的纯培养物。本文对环境基因组的构建及相关分析研究策略的进展进行了综述;同时介绍了其在微生物分类及生态学研究的应用。     

Identification of five human novel genes associated with cell proliferation by cell-based screening from an expressed cDNA ORF library

The development of functional profiling technologies provides opportunity for high-throughput functional genomics studies. We describe a cell-based screening system to identify novel human genes associated with cell proliferation. The method integrates luciferase reporter gene activity, fluorescence stain, automated microscopy and cellular phenotype assays. We successfully used the system to screen 409 novel human genes cloned by our lab and found that 27 genes significantly up-regulated promoter-Renilla luciferase reporter plasmid (pRL) activity. Among them, five genes, TRAF3IP3, ZNF306, ZNF250, SGOL1, and ZNF434, were determined through morphological observation, calcein AM fluorescence stain, MTT assay and cell cycle analysis to be associated with cell proliferation. Furthermore, we showed that the gene TRAF3IP3, which initially was identified to specifically interact with TRAF3, stimulated cell growth by modulating the c-Jun N-terminal kinase (JNK) pathway, and RNAi of TRAF3IP3 confirmed that the effect was physiological and necessary. In summary, we integrated a rapid and efficient system for screening novel growth regulatory genes. Using the new screening system we identified five genes associated with cell proliferation for the first time.     

Expanding functional spaces of enzymes by utilizing whole genome treasure for library construction

A huge database resulted from whole genome sequencings has provided a possibility of new information that is likely to extent the scope and thus changes the way of approach for the functional assigning of putative open reading frames annotated by whole genome sequence analyses. These are mainly realized by ease, one-step identification of putative genes using genomics or proteomics tools. A major challenge remained in biotechnology may translate these informations into better ways to screen or select a gene as a representative sequence. Further attempts to mine the related whole genes or partial DNA fragments from whole genome treasure, and then the incorporation of these sequences into a representative template, will result in the use of genetic information that can be translated into functional proteins or allowed the generation of new lineages as a valuable pool. Such screens enable rapid biochemical analysis and easy isolation of the target activity, thereby accelerating the screening of novel enzymes from the expanded library with related sequences. Information-based PCR amplification of whole genes and reconstitution of functional DNA fragments will provide a platform for expanding the functional spaces of potential enzymes, especially when used mixed- and metagenome as gene resources.     

The hitchhiker's guide to Xenopus genetics

A decade after the human genome sequence, most vertebrate gene functions remain poorly understood, limiting benefits to human health from rapidly advancing genomic technologies. Systematic in vivo functional analysis is ideally suited to the experimentally accessible Xenopus embryo, which combines embryological accessibility with a broad range of transgenic, biochemical, and gain-of-function assays. The diploid X. tropicalis adds loss-of-function genetics and enhanced genomics to this repertoire. In the last decade, diverse phenotypes have been recovered from genetic screens, mutations have been cloned, and reverse genetics in the form of TILLING and targeted gene editing have been established. Simple haploid genetics and gynogenesis and the very large number of embryos produced streamline screening and mapping. Improved genomic resources and the revolution in high-throughput sequencing are transforming mutation cloning and reverse genetic approaches. The combination of loss-of-function mutant backgrounds with the diverse array of conventional Xenopus assays offers a uniquely flexible platform for analysis of gene function in vertebrate development.