锌指核酸酶技术的应用

锌指核酸酶(zinc finger nuclease,ZFN)技术是近年来发展起来的一种对基因组DNA实现靶向修饰的新技术。ZFN通过作用于基因组DNA上特异的靶位点产生DNA双链切口(double strand break,DSB),然后经过非同源末端连接(non-homologous end joining,NHEJ)或同源重组(homologous recombination,HR)途径实现对基因组DNA的靶向敲除或者替换。该技术近些年来已经被广泛应用于基因靶向修饰的研究。本文在简要介绍ZFN技术的基础上,重点综述了目前该技术在基因靶向修饰中的应用研究进展,并同时对该技术目前所需解决的一些问题以及未来的研究方向进行了分析。     

人工核酸酶介导的基因组编辑技术

传统的基因组编辑技术是基于胚胎干细胞和同源重组实现生物基因组定向改造,但是该技术打靶效率低,严重制约了生命科学以及医学的研究.因此,研究新的基因组编辑技术十分重要.人工核酸酶介导的基因组编辑技术是通过特异性识别靶位点造成DNA双链断裂,引起细胞内源性的修复机制实现靶基因的修饰.与传统的基因组编辑技术相比,人工核酸酶技术打靶效率高,这对于基因功能的研究、构建人类疾病动物模型以及探索新型疾病治疗方案有着重要的意义.人工核酸酶技术有3种类型：锌指核酸酶(ZFN)、类转录激活因子核酸酶(TALEN)及规律成簇的间隔短回文重复序列(CRISPR).本文将对以上3种人工核酸酶技术的原理以及在生命科学和医学研究的应用进行综述.     

人工锌指核酸酶介导的基因组定点修饰技术

锌指核酸酶(ZFN)由锌指蛋白(ZFP)结构域和Fok I核酸内切酶的切割结构域人工融合而成,是近年来发展起来的一种可用于基因组定点改造的分子工具。ZFN可识别并结合特定的DNA序列,并通过切割这一序列的特定位点造成DNA的双链断裂(DSB)。在此基础上,人们可以对基因组的特定位点进行各种遗传操作,包括基因打靶、基因定点插入、基因修复等,从而能够方便快捷地对基因组实现靶向遗传修饰。这种新的基因组定点修饰方法的突出优势是适用性好,对物种没有选择性,并且可以在细胞和个体水平进行遗传操作。文章综述了ZFN技术的研究进展及应用前景,重点介绍ZFN的结构与作用机制、现有的靶点评估及锌指蛋白库的构建与筛选方法、基因组定点修饰的策略,以及目前利用这一技术已成功实现突变的物种及内源基因,为开展这一领域的研究工作提供参考。     

《自然-方法学》：锌指核酸酶能以蛋白质形态穿透细胞膜

近期《自然-方法学》（Nature Methods）上一项研究表明用于目标基因组修饰的锌指核酸酶（ZFN）能够以蛋白质的形态穿透细胞膜。这将让ZFN被投递至细胞内的过程变得更简单、更具安全性。     

靶向核酸酶介导基因编辑技术的发展

对目标基因组位点进行靶向修饰一直是基因工程研究的重点。靶向基因编辑技术能够有效地用于建立动物和细胞疾病模型、培育动植物新品种,并具有治疗遗传疾病的重大潜力。近年来靶向核酸酶技术取得了重大的进展,逐渐成为基因编辑的主流工具。综述了锌指核酸酶(ZFN)、类转录激活样效应因子核酸酶(TALEN)、规律成簇间隔短回文重复序列(CRISPR/Cas)这三大靶向基因编辑系统的原理和研究进展,并讨论了其局限性和未来的发展方向。     

利用ZFN敲除转基因猪细胞中多拷贝EGFP基因

锌指核酸酶(zinc finger nuclease,ZFN)是由特异性识别DNA的锌指结构域和Fok I切割结构域组成,能够在基因组特定位点上切割DNA,引起DNA双链断裂(double-strand break,DSB).通过DSB修复机制,可以使基因修饰的效率比传统方法提高102~104倍.目前,利用ZFN对动物内源基因进行敲除的研究较多,但对转基因动物中外源多拷贝基因进行敲除的报道较少.本研究首先利用荧光定量PCR法对本实验室培育的两头转基因猪中增强型绿色荧光蛋白(enhanced green fluorescent protein,EGFP)基因的拷贝数进行鉴定,发现其拷贝数分别为11.95和17.36拷贝;然后将靶向EGFP的一对ZFN转染进拷贝数为17.36的EGFP转基因猪的成纤维细胞中,并通过流式和CEL-1酶切方法检测敲除效率.结果表明,转染400 ng、800 ng和1 200 ng ZFN的切割效率分别为0.97%、1.39%和1.76%,可见随着转染ZFN剂量的增加,ZFN的切割效率逐渐提高.但是,不发绿色荧光的细胞比例却没有明显提高,因此认为,ZFN敲除转基因动物中多拷贝基因的效率还是比较低.     

CRISPR-Cas系统的研究进展及应用

CRISPR-Cas系统是一种靶向基因编辑工具,操作简单,逐渐取代人工锌指核酸酶(ZFN)和类转录激活因子效应物核酸酶(TALEN)而成为近年的研究热点。Cas9蛋白能在一段小的RNA引导下特异性结合并切割DNA,在基因组结构和功能学研究中发挥重要作用。后来发现的Cas13等蛋白能特异性结合和编辑RNA,开启了转录组研究的新篇章。我们对CRISPR-Cas系统近年的研究发现做了简要概述,并对该系统作为一种工具在基础研究、生物工程、疾病治疗上的应用进行了总结。     

哺乳动物基因组靶向修饰阳性细胞富集的报告载体系统研究进展

基因组靶向修饰技术对基因功能研究、基因治疗以及转基因育种研究都具有重要的意义和价值。近年来发展起来的人工核酸酶如ZFNs、TALENs和CRISPR/Cas9等的应用大大提高了基因组靶向修饰的效率。但是由于核酸酶表达载体转染效率、核酸酶表达效率及活性以及基因组被打靶后的修复效率等因素在一定程度上制约着基因组靶向修饰阳性细胞的获得。因此富集和筛选基因组靶向修饰阳性细胞是一个亟待解决的问题。报告载体系统可以间接地反映核酸酶的工作效率并有效富集核酸酶修饰的阳性细胞,进而提高基因组靶向修饰阳性细胞的富集和筛选效率。本文主要针对由非同源末端连接(Non-homologous end joining,NHEJ)和单链退火(Single-strand annealing,SSA)两种修复机制分别介导的报告载体系统的原理和应用进行了详细的介绍,以期为以后的相关研究提供借鉴和参考。     

利用ZFN删除转基因猪细胞中的多拷贝EGFP基因

锌指核酸酶（zinc finger nuclease, ZFN）是由特异性识别DNA的锌指结构域和Fok I切割结构域组成,能够在基因组特定位点上切割DNA,引起DNA双链断裂（double-strand break, DSB）. 通过DSB修复机制,可以使基因修饰的效率比传统方法提高102～104倍．目前,利用ZFN对动物内源基因进行敲除的研究较多,但对转基因动物中外源多拷贝基因进行敲除的报道较少．本研究首先利用荧光定量PCR法对本实验室培育的两头转基因猪中增强型绿色荧光蛋白（enhanced green fluorescent protein, EGFP）基因的拷贝数进行鉴定,发现其拷贝数分别为11.95和17.36拷贝;然后将靶向EGFP的一对ZFN转染进拷贝数为1736的EGFP转基因猪的成纤维细胞中,并通过流式和CEL-1酶切方法检测敲除效率. 结果表明,转染400 ng、800 ng和1 200 ng ZFN的切割效率分别为0.97%、1.39%和1.76%,可见随着转染ZFN剂量的增加,ZFN的切割效率逐渐提高．但是,不发绿色荧光的细胞比例却没有明显提高,因此认为,ZFN敲除转基因动物中多拷贝基因的效率还是比较低．     

新型靶向基因组编辑技术研究进展

传统的靶向基因组编辑技术改造基因效率非常低,严重制约了基础研究和临床应用。因此,新的靶向基因组编辑工具的研究显得非常重要,以此来提高基因原位修复、定点整合及高通量基因敲除的效率。主要论述了近年来发现的新型靶向基因组编辑技术即锌指核酸酶(ZFN)、转录激活子样效应因子核酸酶(TALENs)、规律成簇间隔短回文重复(CRISPR)/Cas系统。从它们的发现、结构和研究进展及应用前景等方面进行了总结;通过比较三者的优缺点,发现规律成簇间隔短回文重复(CRISPRs)具有明显的优点。     

Homologous recombination efficiency enhanced by inhibition of MEK and GSK3β

Homologous recombination in embryonic stem cells (ESCs) is widely utilized in genome engineering, particularly in the generation of gene targeted mice. However, genome engineering is often plagued by the problem of low homologous recombination efficiency. In this study, we developed a novel method to increase the efficiency of homologous recombination in ESCs by changing its culture conditions. By comparing the efficiency of different ESCs in various culture conditions, we determined that chemicals that inhibit the MEK and GSK3β pathways (2i condition) enhance homologous recombination and eliminate differences in efficiencies among cell lines. Analysis of gene expression patterns in ESCs maintained in different culture conditions has identified several homologous recombination‐related candidates, including the pluripotent markers Eras and Tbx3. The results of this study suggest that homologous recombination is associated with ESC pluripotency. genesis 52:889–896, 2014. © 2014 Wiley Periodicals, Inc.     

Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference

The discovery that the machinery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 bacterial immune system can be re-purposed to easily create deletions, insertions and replacements in the mammalian genome has revolutionized the field of genome engineering and re-invigorated the field of gene therapy. Many parallels have been drawn between the newly discovered CRISPR-Cas9 system and the RNA interference (RNAi) pathway in terms of their utility for understanding and interrogating gene function in mammalian cells. Given this similarity, the CRISPR-Cas9 field stands to benefit immensely from lessons learned during the development of RNAi technology. We examine how the history of RNAi can inform today''s challenges in CRISPR-Cas9 genome engineering such as efficiency, specificity, high-throughput screening and delivery for in vivo and therapeutic applications.     

Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases

The ability to specifically engineer the genome of living cells at precise locations using rare-cutting designer endonucleases has broad implications for biotechnology and medicine, particularly for functional genomics, transgenics and gene therapy. However, the potential impact of chromosomal context and epigenetics on designer endonuclease-mediated genome editing is poorly understood. To address this question, we conducted a comprehensive analysis on the efficacy of 37 endonucleases derived from the quintessential I-CreI meganuclease that were specifically designed to cleave 39 different genomic targets. The analysis revealed that the efficiency of targeted mutagenesis at a given chromosomal locus is predictive of that of homologous gene targeting. Consequently, a strong genome-wide correlation was apparent between the efficiency of targeted mutagenesis (≤ 0.1% to ≈ 6%) with that of homologous gene targeting (≤ 0.1% to ≈ 15%). In contrast, the efficiency of targeted mutagenesis or homologous gene targeting at a given chromosomal locus does not correlate with the activity of individual endonucleases on transiently transfected substrates. Finally, we demonstrate that chromatin accessibility modulates the efficacy of rare-cutting endonucleases, accounting for strong position effects. Thus, chromosomal context and epigenetic mechanisms may play a major role in the efficiency rare-cutting endonuclease-induced genome engineering.     

W::Neo: a novel dual-selection marker for high efficiency gene targeting in Drosophila

We have recently developed a so-called genomic engineering approach that allows for directed, efficient and versatile modifications of Drosophila genome by combining the homologous recombination (HR)-based gene targeting with site-specific DNA integration. In genomic engineering and several similar approaches, a "founder" knock-out line must be generated first through HR-based gene targeting, which can still be a potentially time and resource intensive process. To significantly improve the efficiency and success rate of HR-based gene targeting in Drosophila, we have generated a new dual-selection marker termed W::Neo, which is a direct fusion between proteins of eye color marker White (W) and neomycin resistance (Neo). In HR-based gene targeting experiments, mutants carrying W::Neo as the selection marker can be enriched as much as fifty times by taking advantage of the antibiotic selection in Drosophila larvae. We have successfully carried out three independent gene targeting experiments using the W::Neo to generate genomic engineering founder knock-out lines in Drosophila.     

Expanding the CRISPR toolbox for Chinese hamster ovary cells with comprehensive tools for Mad7 genome editing

The production of high-value biopharmaceuticals is dominated by mammalian production cells, particularly Chinese hamster ovary (CHO) cells, which have been widely used and preferred in manufacturing processes. The discovery of CRISPR-Cas9 significantly accelerated cell line engineering advances, allowing for production yield and quality improvements. Since then, several other CRISPR systems have become appealing genome editing tools, such as the Cas12a nucleases, which provide broad editing capabilities while utilizing short guide RNAs (gRNAs) that reduce the complexity of the editing systems. One of these is the Mad7 nuclease, which has been shown to efficiently convey targeted gene disruption and insertions in several different organisms. In this study, we demonstrate that Mad7 can generate indels for gene knockout of host cell proteins in CHO cells. We found that the efficiency of Mad7 depends on the addition of protein nuclear localization signals and the gRNAs employed for genome targeting. Moreover, we provide computational tools to design Mad7 gRNAs against any genome of choice and for automated indel detection analysis from next-generation sequencing data. In summary, this paper establishes the application of Mad7 in CHO cells, thereby improving the CRISPR toolbox versatility for research and cell line engineering.     

CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production

Cyanobacteria hold promise as a cell factory for producing biofuels and bio-derived chemicals, but genome engineering of cyanobacteria such as Synechococcus elongatus PCC 7942 poses challenges because of their oligoploidy nature and long-term instability of the introduced gene. CRISPR-Cas9 is a newly developed RNA-guided genome editing system, yet its application for cyanobacteria engineering has yet to be reported. Here we demonstrated that CRISPR-Cas9 system can effectively trigger programmable double strand break (DSB) at the chromosome of PCC 7942 and provoke cell death. With the co-transformation of template plasmid harboring the gene cassette and flanking homology arms, CRISPR-Cas9-mediated DSB enabled precise gene integration, ameliorated the homologous recombination efficiency and allowed the use of lower amount of template DNA and shorter homology arms. The CRISPR-Cas9-induced cell death imposed selective pressure and enhanced the chance of concomitant integration of gene cassettes into all chromosomes of PCC 7942, hence accelerating the process of obtaining homogeneous and stable recombinant strains. We further explored the feasibility of engineering cyanobacteria by CRISPR-Cas9-assisted simultaneous glgc knock-out and gltA/ppc knock-in, which improved the succinate titer to 435.0±35.0 μg/L, an ≈11-fold increase when compared with that of the wild-type cells. These data altogether justify the use of CRISPR-Cas9 for genome engineering and manipulation of metabolic pathways in cyanobacteria.     

Implementing CRISPR-Cas technologies in conventional and non-conventional yeasts: Current state and future prospects

Within five years, the CRISPR-Cas system has emerged as the dominating tool for genome engineering, while also changing the speed and efficiency of metabolic engineering in conventional (Saccharomyces cerevisiae and Schizosaccharomyces pombe) and non-conventional (Yarrowia lipolytica, Pichia pastoris syn. Komagataella phaffii, Kluyveromyces lactis, Candida albicans and C. glabrata) yeasts.Especially in S. cerevisiae, an extensive toolbox of advanced CRISPR-related applications has been established, including crisprTFs and gene drives. The comparison of innovative CRISPR-Cas expression strategies in yeasts presented here may also serve as guideline to implement and refine CRISPR-Cas systems for highly efficient genome editing in other eukaryotic organisms.     

转座子Sleeping Beauty和PiggyBac

近10年来,得益于转座子Sleeping Beauty(SB)和PiggyBac(PB)的发现和完善,转座子作为一种遗传工程工具在脊椎动物的基因遗传研究中得到广泛应用.SB和PB宿主范围极其广泛,从单细胞生物到哺乳动物都能够发挥作用.转座过程需要转座序列和转座酶的存在,类似于"剪切"、"粘贴"的方式.转座子载体系统转座时可携带一段外源DNA序列,利用这一特性可以用于实现目的基因的转移,现已广泛用于转基因动物、基因功能研究、基因治疗等领域.当转座系统与基因捕获技术相结合,不仅可研究插入突变基因的功能,还能通过所携带的报告基因获得捕获基因的表达图谱.作为非病毒载体的SB和PB转座系统,由于具有高容量、高效率和高安全性等优势,并且PB在转座后不留任何足迹,不会造成遗传物质的不可预测改变,在动物基因工程以及基因治疗方面具有诱人的前景.