植物基因同源重组研究现状

同源重组是普遍存在的生物学现象,从噬菌体、细菌到真核生物均有存在。它对生物的遗传与变异具有重大影响,一直是生物学家研究的热点。本文从染色体外同源重组、染色体内同源重组以及基因打靶三个方面综述了同源重组在植物方面的研究现状。从分子水平上较详尽的介绍了同源重组发生的机制以及同源重组在生物领域的应用、前景展望及其存在的局限性。     

植物基因打靶技术

基因打靶是反向遗传学的基础工具,它通过同源重组置换染色体内的基因用于复杂基因组的基因功能分析。但是,在植物中,外源DNA的插入主要是非序列依赖的非同源末端连接方式,基因打靶频率很低,只有10-5～10-4的水平。综述了近年来为了提高植物基因打靶频率,研究人员的工作和最新进展 。     

植物基因同源重组研究现状

同源重组是普遍存在的生物学现象,从噬菌体、细菌到相传真核生物均有存在。它对生物的遗传与变异具有重大影响,一直是生物学家研究的热点。本文从染色体外同源重组、染色体内同源重组以及基因打靶三个方面综述了同源重组在植物方面的研究现状。从分子水平上较详尽的介绍了同源重组发生的机制以及同源重组在生物领域的应用、前景展望及其存在的局限性。     

一种新的基于Red重组及I-Sec I体内切割的大肠杆菌基因组无痕删减方法

目前常用的基因修饰方法是在Red同源重组介导下,电转线性PCR片段替换染色体上指定序列。因PCR过程错误掺入,该方法常常会在同源序列部位产生一些突变。为了避免此类突变,我们建立了一种新的无痕删除方法。首先将含有抗性标记(两侧带有I-Sec I识别位点)的线性DNA电转到Red重组感受态细胞内,用抗性基因替换基因组上指定序列;然后,将携带融合同源臂(两侧带有I-Sec I位点)的供体质粒导入上述细胞,诱导表达I-Sec I内切酶切割供体质粒释放同源片段,同时切除染色体上抗性基因产生双链断裂,通过分子间同源重组实现无痕删除。我们应用该方法连续删除了大肠杆菌DH1基因组上11个非必需区,使基因组减小10.59%。PCR测序证明所有删减区域同源臂未发生突变,基因组重测序证明指定区域被删除。删减菌的生长变化不大,但耐酸能力有所改变,并对番茄红素合成有不同影响。     

马尔尼菲青霉基于pkuB基因缺失的高效基因打靶系统构建

马尔尼菲青霉是温度依赖双相性条件性致病真菌,可感染免疫缺陷人群,区域流行于东南亚和我国南方。马尔尼菲青霉已成为研究真菌双相形态转换和病原-宿主相互作用分子机制的模式系统。功能基因组学研究为深入探讨马尔尼菲青霉双相转换和致病分子机制提供了线索,大量的候选基因功能需要高通量的基因修饰方法验证。在许多真菌中已建立基于阻断DNA非同源重组修复途径提高基因打靶效率的实验研究模型。本文报道在马尔尼菲青霉中通过缺失马尔尼菲青霉非同源重组修复途径的关键组分PKUB同源基因pkuB构建了一个高效基因打靶系统。结果表明,以pkuB基因缺失菌株(△pkuB)为出发菌株能降低外源DNA片段的非同源末端连接重组的概率而显著提高基因打靶效率,pkuB基因缺失不影响菌落形态和双相转换能力。高效基因打靶分子遗传实验模型的建立为大规模进行马尔尼菲青霉基因功能研究提供了有力的工具。     

基因组编辑技术中供体DNA类型及选择北大核心CSCD

基因组编辑技术能够实现基因组的精确修饰和改造,是后基因组时代研究基因功能和遗传信息的主要手段。传统的基因打靶技术通过低效率的细胞自发同源重组实现目的基因的定点修饰。真核细胞中DNA双链断裂介导的同源重组效率远高于自发同源重组,利用人工核酸内切酶特异性地在基因组靶序列处引入双链断裂,通过提供适当形式的、含有一定长度同源臂的供体DNA,能够实现相对高效的基因组靶向编辑。本文系统总结了环状质粒、线性化质粒、聚合酶链式反应产物及单链寡聚脱氧核苷酸4种类型的供体DNA在基因组精确编辑研究中的应用及候选原则,以期为以后相关研究中供体DNA的选择、设计提供参考和借鉴。     

基因组编辑技术中供体DNA类型及选择

基因组编辑技术能够实现基因组的精确修饰和改造,是后基因组时代研究基因功能和遗传信息的主要手段。传统的基因打靶技术通过低效率的细胞自发同源重组实现目的基因的定点修饰。真核细胞中DNA双链断裂介导的同源重组效率远高于自发同源重组,利用人工核酸内切酶特异性地在基因组靶序列处引入双链断裂,通过提供适当形式的、含有一定长度同源臂的供体DNA,能够实现相对高效的基因组靶向编辑。本文系统总结了环状质粒、线性化质粒、聚合酶链式反应产物及单链寡聚脱氧核苷酸4种类型的供体DNA在基因组精确编辑研究中的应用及候选原则,以期为以后相关研究中供体DNA的选择、设计提供参考和借鉴。     

基因打靶技术的研究进展

基因打靶技术是20世纪80年代发展起来的新技术,是一种利用DNA同源重组原理和胚胎干细胞(ES细胞)技术按定向组合的方式改变生物活体遗传信息的试验手段,具有广阔的应用前景。对基因打靶技术原理、步骤、条件性基因打靶以及应用进行综述。     

小鼠MPI基因的打靶载体的构建和筛选

目的　构建小鼠MPI基因的基因打靶载体转染ES细胞 ,构建用于同源重组筛选的对照载体。方法根据计算机分析小鼠MPI基因的基因组序列 ,构建用于同源重组载体的长臂和短臂并且转染小鼠ES细胞 ,经抗性筛选后得到阳性克隆 ,抽提基因组DNA后用PCR的方法进行重组子的初步筛选。结果　成功构建了MPI基因的基因打靶载体并且摸索了用PCR的方法进行重组细胞初步筛选的方法。结论　这个载体的构建为MPI基因功能的研究打下了基础 ,同时用PCR方法进行初步筛选大大减少了Southern杂交的工作量 ;利用实验小鼠来研究印迹基因是非常有效的方法 ,它不仅能了解印迹基因在小鼠生长发育过程中的功能 ,而且进而有助于研究人的相应印迹区。     

Red同源重组技术研究进展

伴随着分子生物学的发展,一种基于λ噬菌体Red重组酶的同源重组系统已应用于大肠杆菌基因工程研究。Red重组系统由三种蛋白组成:Exo蛋白是一种核酸外切酶,结合在双链DNA的末端,从5′端向3′端降解DNA,产生3′突出端;Beta蛋白结合在单链DNA上,介导互补单链DNA退火;Gam蛋白可与RecBCD酶结合,抑制其降解外源DNA的活性。Red同源重组技术具有同源序列短(40～60bp)、重组效率高的特点。这种技术可在DNA靶标分子的任意位点进行基因敲除、敲入、点突变等操作,无需使用限制性内切酶和连接酶。此外,这种新型重组技术可直接将目的基因克隆于载体上,目的基因既可来源于细菌人工染色体也可是基因组DNA。Red同源重组技术使难度较大的基因工程实验顺利进行,大大推动功能基因组研究的发展。     

The structure-specific endonuclease Ercc1-Xpf is required for targeted gene replacement in embryonic stem cells.

The Ercc1-Xpf heterodimer, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair and homologous recombination. Ercc1-Xpf incises double-stranded DNA at double-strand/single-strand junctions, making it an ideal enzyme for processing DNA structures that contain partially unwound strands. Here we demonstrate that although Ercc1 is dispensable for recombination between sister chromatids, it is essential for targeted gene replacement in mouse embryonic stem cells. Surprisingly, the role of Ercc1-Xpf in gene targeting is distinct from its previously identified role in removing nonhomologous termini from recombination intermediates because it was required irrespective of whether the ends of the DNA targeting constructs were heterologous or homologous to the genomic locus. Our observations have implications for the mechanism of gene targeting in mammalian cells and define a new role for Ercc1-Xpf in mammalian homologous recombination. We propose a model for the mechanism of targeted gene replacement that invokes a role for Ercc1-Xpf in making the recipient genomic locus receptive for gene replacement.     

Is it possible to improve homologous recombination in Chlamydomonas reinhardtii?

Targeted modification of the genome has long been an aim of many geneticists and biotechnologists. Gene targeting is a main molecular tool to examine biological effects of genes in a controlled environment. Effective gene targeting depends on the frequency of homologous recombination that is indispensable for the insertion of foreign DNA into a specific sequence of the genome. The main problem associated with the development of an optimal procedure for gene targeting in a particular organism is the variability of homologous recombination (HR) in different species. Chlamydomonas reinhardtii is an attractive model system for the study of many cellular processes and is also an interesting object for the biotechnology industry. In spite of many advantages of this model system, C. reinhardtii does not readily express heterologous genes and does not allow targeted integration of foreign DNA into its genome easily. This paper compares data obtained from several different experiments designed for improving gene targeting in different organisms and reviews the suitability of particular techniques in C. reinhardtii cells. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.     

Stimulation of RecA-mediated D-loop formation by oligonucleotide-directed triple-helix formation: guided homologous recombination (GOREC)

Oligonucleotide-directed triple helix formation provides an elegant rational basis for gene-specific DNA targeting and has been widely used to interfere with gene expression ("antigene" strategies) and as a molecular tool for biological studies. Various strategies have been developed to introduce sequence modifications in genomes. However, the low efficiency of the overall process in eucaryotic cells impairs efficient recovery of recombinant genomes. Since one limiting step in homologous recombination is the targeting to the homologous sequence, we have tested the contribution of an oligonucleotide-directed triple helix formation on the RecA-dependent association of an oligonucleotide and its homologous target on duplex DNA (D-loop formation). For this study, the recombinant ssDNA fragment was noncovalently associated to a triple helix-forming oligonucleotide. The physicochemical and biochemical characteristics of the triple helix and D-loop structures formed by the complex molecules in the presence or in the absence of RecA protein were determined. We have demonstrated that the triple helix-forming oligonucleotide increases the efficiency of D-loop formation and the RecA protein speeds up also the triple helix formation. The so-called "GOREC" (for guided homologous recombination) approach can be developed as a novel tool to improve the efficiency of directed mutagenesis and gene alteration in living organisms.     

利用Red同源重组系统构建兔次黄嘌呤-鸟嘌呤磷酸核糖转移酶基因打靶载体

利用EL350基因工程菌进行同源重组,成功进行基因敲除已有报道,但利用该系统进行兔次黄嘌呤-鸟嘌呤磷酸核糖转移酶(Hypoxanthine guanine phosphoribosyl transferase,HPRT)基因突变和基因打靶方面的研究还没有报道。本实验首先在已经筛选到含有兔全长HPRT基因BAC克隆（LBNL1-304M19）的基础上,利用Red重组系统,通过Gap-Repair方式从此克隆上将一段47Kb无启动子的HPRT基因组片段（不含有第1个外显子）克隆到pBACLinkSp质粒上,产生pBACLinkSp-rHPRT质粒。然后基于pBACLinkSp-rHPRT质粒,设计不同的同源臂,从而删除了HPRT基因的不同编码区,成功构建了三个不同的HPRT基因打靶载体。同时对利用同源重组技术敲除不同大小的DNA片段的效率进行了研究。基于本实验所构建的三个不同的兔HPRT基因打靶载体,为探索兔成纤维细胞和胚胎干细胞基因打靶的适宜条件,及进一步获得兔HPRT基因敲除动物疾病模型奠定了基础。     

Choreography of recombination proteins during the DNA damage response

Genome integrity is frequently challenged by DNA lesions from both endogenous and exogenous sources. A single DNA double-strand break (DSB) is lethal if unrepaired and may lead to loss of heterozygosity, mutations, deletions, genomic rearrangements and chromosome loss if repaired improperly. Such genetic alterations are the main causes of cancer and other genetic diseases. Consequently, DNA double-strand break repair (DSBR) is an important process in all living organisms. DSBR is also the driving mechanism in most strategies of gene targeting, which has applications in both genetic and clinical research. Here we review the cell biological response to DSBs in mitotically growing cells with an emphasis on homologous recombination pathways in yeast Saccharomyces cerevisiae and in mammalian cells.     

利用Red重组系统快速构建基因打靶载体

基因敲除小鼠模型是在哺乳动物体内研究基因功能最可靠的方法之一。利用常规的分子克隆的方法构建基因打靶载体往往工作周期长,对于难度特别大的基因有时甚至无法完成打靶载体的构建。通过合理应用Red重组系统和低拷贝中间载体,利用50bp的同源重组序列直接从BAC载体中克隆了长片段的小鼠基因组序列;将得到的基因组序列再次通过重组和改造,构建了Gpr56等基因的完全敲除并带有报告基因的打靶载体,实现了打靶载体的快速构建。     

Targeted gene conversion induced by triplex-directed psoralen interstrand crosslinks in mammalian cells

Correction of a defective gene is a promising approach for both basic research and clinical gene therapy. However, the absence of site-specific targeting and the low efficiency of homologous recombination in human cells present barriers to successful gene targeting. In an effort to overcome these barriers, we utilized triplex-forming oligonucleotides (TFOs) conjugated to a DNA interstrand crosslinking (ICL) agent, psoralen (pTFO-ICLs), to improve the gene targeting efficiency at a specific site in DNA. Gene targeting events were monitored by the correction of a deletion on a recipient plasmid with the homologous sequence from a donor plasmid in human cells. The mechanism underlying this event is stimulation of homologous recombination by the pTFO-ICL. We found that pTFO-ICLs are efficient in inducing targeted gene conversion (GC) events in human cells. The deletion size in the recipient plasmid influenced both the recombination frequency and spectrum of recombinants; i.e. plasmids with smaller deletions had a higher frequency and proportion of GC events. The polarity of the pTFO-ICL also had a prominent effect on recombination. Our results suggest that pTFO-ICL induced intermolecular recombination provides an efficient method for targeted gene correction in mammalian cells.     

TCDD-induced homologous recombination: the role of the Ah receptor versus oxidative DNA damage

The environmental toxicant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) elicits numerous biological responses including carcinogenicity. The molecular mechanism by which TCDD exerts its tumorigenic effects is unclear, since it does not directly damage DNA. TCDD-initiated toxicity can be mediated by the aryl hydrocarbon receptor (AhR) pathway and/or via increased oxidative stress. DNA damage, including DNA oxidation, can induce DNA double-strand breaks, which can be repaired through homologous recombination. Excessive DNA double-strand breaks may promote aberrant DNA recombination, which can lead to detrimental genetic changes and ultimately to carcinogenesis. TCDD has been shown to induce homologous recombination but the molecular mechanism mediating these events are unknown. To investigate the role of the AhR and oxidative DNA damage in mediating TCDD-induced homologous recombination we used a Chinese hamster ovary (CHO) cell line containing a neo direct repeat recombination substrate (CHO 3-6). CHO 3-6 cells were exposed to TCDD (50, 500 or 1000 pM) in the presence or absence of an AhR antagonists (0.1 microM alpha-naphthoflavone (alpha-NF)) for 6 or 24 h and 2 weeks later homologous recombination frequencies were determined by counting the number of neo expressing, G418-resistant colonies per live cells plated. TCDD-initiated DNA oxidation was determined by measuring the formation of 8-hydroxy-2'-deoxyguanosine via HPLC and electrochemical detection. Exposure to 500 pM TCDD for 24 h significantly increased the frequency of homologous recombination. Southern blot analysis on G418-resistant colonies determined that TCDD induced both conservative gene conversion events and deletion events. DNA oxidation was not increased in cells exposed to TCDD for either 6 or 24 h. However, alpha-naphthoflavone exposure resulted in a significant decrease in TCDD-induced homologous recombination frequency. These results suggest that TCDD-initiated homologous recombination in CHO 3-6 cells is mediated by the AhR and not via increased oxidative stress.     

DNA oligonucleotide-assisted genetic manipulation increases transformation and homologous recombination efficiencies: Evidence from gene targeting of Dictyostelium discoideum

Artificial gene alteration by homologous recombination in living cells, termed gene targeting, presents fundamental and considerable knowledge of in vivo gene function. In principle, this method can possibly be applied to any type of genes and transformable cells. However, its success is limited due to a low frequency of homologous recombination between endogenous targeted gene and exogenous transgene. Here, we describe a general gene-targeting method in which co-transformation of DNA oligonucleotides (oligomers) could significantly increase the homologous recombination frequency and transformation efficiency. The oligomers were simply designed such that they were identical to both the ends of the homologous flanking regions of the targeting construct. Using this strategy, both targeted alleles of diploid cells were simultaneously replaced in a single transformation procedure. Thus, the simplicity and versatility of this method applicable to any type of cell may increase the application of gene targeting.     

影响动物细胞同源重组发生与基因打靶效率的分子机制

真核细胞的基因打靶是基因结构与功能研究的一种非常有价值的技术,也是可应用于基因治疗的具有潜力的工具。有2个限制因素束缚真核细胞基因打靶的发展,即同源重组(HR)率非常低而随机整合率非常高。通过特定基因的过表达或表达干涉,使一些参与DNA重组的蛋白表达水平瞬间改变,可能会增加HR率,降低随机整合率。本文列举了一些与HR相关的候选基因,详细介绍了其中的Rad52上位簇基因,还讨论了打靶载体的设计与修饰、DNA转染方法的有效性等。