基于CRISPR/Cas9系统对斑马鱼hoxb4基因的编辑及其突变体基因型的初筛

采用高效基因编辑系统CRISPR/Cas9构建hoxb4基因敲除斑马鱼模型,进行hoxb4基因功能的研究。根据hoxb4基因的一号外显子的正义链及反义链设计3个长20 bp的sg RNA,分别靶向ExonⅠ的192#位点,244#位点及313#位点。化学合成sg RNA的寡核苷酸序列,经过酶切克隆进p T7-g RNA质粒中,构建g RNA的体外转录载体并通过体外转录得到靶位点的g RNA。将质粒p SP6-2s NLS-sp Cas9线性化然后在体外转录得到Cas9的m RNA并进行加A尾,将以上靶位点的g RNA与Cas9的m RNA共注射入单细胞期的斑马鱼胚胎内,提取基因组DNA,PCR扩增出目的基因片段并使用T7EI酶切测效,最后将PCR产物连入p MD19-T simple载体中,挑取阳性克隆进行菌落PC R鉴定,然后经Sanger测序检测突变类型。结果显示,靶位点的sg RN A寡核苷酸双链成功连入p T7-g RNA质粒中且序列正确;其中靶向ExonⅠ的313#位点的sg RNA可成功编辑斑马鱼hoxb4基因,T7 EⅠ检测其敲除效率高达26.5%,并测序得到4种阳性突变型。通过CRISPR/Cas9系统成功编辑斑马鱼hoxb4基因并测序鉴定其突变类型,为HOXb4基因功能的研究提供了可靠的基因敲除方法。     

斑马鱼心脏发育候选基因Titin-Cap的CRISPR/Cas9打靶有效性分析

CRISPR/Cas9基因打靶技术是近几年发展起来的一种高效率的定向打靶技术,被认为是遗传领域的革命性技术。Titin-Cap基因是本实验室已初步鉴定的斑马鱼心脏发育候选基因,且国内外目前尚无斑马鱼Titin-Cap基因的敲除品系。为了研究Titin-Cap基因在心脏发育过程中的作用机制,我们利用CRISPR/Cas9基因打靶技术建立斑马鱼Titin-Cap基因的敲除品系。测序结果显示,注射了CRISPR/Cas9 gRNA的胚胎出现双峰,说明在打靶位点附近出现了碱基缺失或插入,证明我们设计的gRNA是有效的。对F0代突变体成鱼的筛选中,测序结果同样显示有阳性结果。这些结果说明用CRISPR/Cas9基因打靶技术成功敲除了斑马鱼Titin-Cap基因,获得了Titin-Cap基因敲除的嵌合体斑马鱼。     

基于新的CRISPR/Cas9技术实现斑马鱼LHX9基因的快速编辑及对F0突变体性腺发育的初筛

目的:CRISPR/Cas9系统在斑马鱼的反向遗传学中的到了广泛应用,但突变基因的表型观察往往需要在突变鱼系的F1中进行,费时较长。LHX9作为LIM家族的一种转录因子,在胚胎早期的泌尿生殖嵴中有广泛分布;且LHX9基因敲除的小鼠存在性腺发育不良。本研究拟通过一种新的CRISPR/Cas9基因编辑技术,采用四条sgRNA对LHX9基因进行VASA转基因斑马鱼的基因敲除,以观察该基因缺陷对斑马鱼性腺发育的影响。方法:利用新的CRISPR/Cas9技术,设计四条针对斑马鱼LHX9基因3号外显子的20bp的sgRNA,通过非克隆体外转录得到靶位点的四条sgRNA。将以上靶位点的四条sgRNA与Cas9核酸酶蛋白同时注射入单细胞期的斑马鱼胚胎内,利用PCR鉴定突变型类型和突变比例。通过对LHX9基因突变体的VASA转基因斑马鱼进行荧光观察,发现LHX9基因缺陷的斑马鱼性腺发育的情况。结果:靶向Exon 3的四条sgRNA可成功编辑斑马鱼LHX9基因,敲除效率高达82%,Sanger测序发现产生10种不同的移码突变类型。通过该方法对VASA转基因斑马鱼的LHX9基因进行编辑,发现LHX9基因突变导致dph6的的斑马鱼原始生殖细胞增殖和迁移受到影响。结论:基于4条sgRNA注射的CRISPR/Cas9技术,可以快速地产生具有突变表型的G0斑马鱼,具有应用潜力。LHX9基因敲除导致原始生殖细胞的发育和迁移受到影响,提示该基因参与了斑马鱼早期性腺的发育。     

斑马鱼miR-196a-1基因敲除品系的构建

microRNA(miRNA)是一类内生的、长度约为19～23个核苷酸的非编码RNA,通过影响mRNA的稳定性和翻译,来参与基因表达的转录后调控。生物信息学分析表明该基因在各个物种中高度保守。为了阐明该基因在肠道发育中的作用,本文利用Cloning free CRISPR/Cas9基因编辑技术构建miR-196a-1基因敲除的斑马鱼品系。首先通过分析软件筛选出斑马鱼miR-196a-1基因的两个敲除位点,两个敲除位点相隔132 bp,利用PCR技术扩增miR-196a-1的向导DNA,再以向导DNA为模板转录得到miR-196a-1的sgRNA,将miR-196a-1基因的sgRNA和Cas9蛋白共同注射到斑马鱼胚胎1细胞期胚胎中。斑马鱼胚胎发育到36 hpf后进行基因编辑的有效性检测,研究结果显示,miR-196a-1基因出现102 bp碱基的缺失,表明CRISPR/Cas9系统对miR-196a-1基因的敲除有效。对其F0代、F1代、F2代进行筛选,成功获得斑马鱼miR-196a-1基因敲除品系,为研究miR-196a-1在肠道发育中的作用奠定了基础。     

针对Fbxl5基因关键结构域F-box的Crispr/Cas9打靶有效性分析

为了在动物体内研究Fbxl5基因是通过什么机制导致斑马鱼心脏出现突变表型,本文利用近几年兴起的CRISPR/Cas9打靶技术建立斑马鱼Fbxl5基因敲除品系。本文将打靶位点定位于Fbxl5的F-box结构域,也就是Fbxl5的第五号外显子上。首先经过基因打靶网站分析筛选出针对Fbxl5基因F-box结构域最适合的打靶位点,扩增出Fbxl5基因CRISPR/Cas9打靶双链DNA,并转录为RNA,与Hcas9共注射至斑马鱼胚胎。最后,在注射48 h后对Fbxl5基因CRISPR/Cas9打靶的有效性进行检测。首先在注射48 h之后收集胚胎提取基因组DNA,用特异性引物进行PCR扩增;将纯化后的Fbxl5基因PCR产物连接到p MD18-T载体,再经质粒提取,测序分析,通过与WT斑马鱼基因组序列进行比对发现Fbxl5-9号在PAM序列AGG下游缺失了4个碱基。证明该CRISPR/Cas9系统在敲除心脏发育候选基因Fbxl5是有效的,该研究为最终获得Fbxl5基因敲除斑马鱼奠定了良好的基础。     

CRISPR/Cas9介导的斑马鱼基因敲入技术研究进展

规律性成簇间隔的短回文重复序列(clustered regularly interspaced palindromic repeats,CRISPR)及相关蛋白组成的CRISPR/Cas9系统作为细菌和古细菌一种适应性免疫防御体系,近年被用于多个物种的精准基因编辑。作为重要的脊椎动物发育生物学模式生物,斑马鱼具有发育快、易饲养、繁殖力强和胚胎透明易观察等众多优点,因此以斑马鱼为模型也开展了许多基于基因编辑的相关研究。相较于基因敲除高效的随机突变,精准基因敲入(knock-in,KI)的低效率一直是斑马鱼基因编辑领域的短板。本文综述了在斑马鱼中使用CRISPR/Cas9系统进行基因敲入的相关研究进展,为优化精准敲入效率以及建立斑马鱼疾病模型等方面提供借鉴。     

利用 CRISPR／Cas9敲除大鼠胰岛素受体底物1（Ir s1）基因

目的：为研究胰岛素受体底物1（Irs1）基因与代谢病之间的关系,我们利用CRISPR/Cas9系统敲除大鼠Irs1基因,为研究代谢病提供基因敲除大鼠。方法针对Irs1第一外显子,设计CRISPR/Cas9作用靶点,构建sgRNA表达质粒。利用T7 RNA聚合酶体外转录sgRNA和Cas9。将Cas9 mRNA和sgRNA混合物注射入SD大鼠的受精卵中,实现靶基因敲除。用T7 EN1实验初步检测靶基因的修饰情况,再经过测序分析确定突变。结果获得了5个在Irs1基因突变的首建鼠,突变效率为83％。结论得到了稳定遗传的Irs1基因敲除大鼠。     

基于CRISPR/Cas9技术敲除SAMHD1肝癌细胞系的构建及对增殖的影响

运用CRISPR/Cas9基因编辑技术,建立SAMHD1基因敲除的Huh7细胞系,并检测敲除SAMHD1基因后对人肝癌细胞Huh7细胞增殖的影响.针对SAMHD1基因作用的功能区域,设计靶向SAMHD1的小向导sgRNA(Small Guide RNA).构建lentiCRISPRv2-SAMHDl-gRNA重组质粒转化后测序.筛选稳定敲除SAMHD1的稳定细胞系并测序鉴定.采用克隆形成实验分析基因SAMHD1敲除后肝癌细胞Huh7细胞的增殖能力.测序结果显示lentiCRISPRv2-SAMHDl-gRNA载体构建成功.Western blot结果和测序结果表明成功构建敲除SAMHD1的Huh7稳定细胞系.克隆形成实验结果表明,相对于Huh7-WT细胞,Huh7-KO SA-MHD1的细胞增殖能力增强(P＜0.01).成功构建基于CRISPR/Cas9技术敲除SAMHD1基因的Huh7细胞系,SAMHD1的表达缺失促进肝癌细胞的增殖.     

利用CRISPR/Cas9技术构建大鼠L2细胞α-ENaC基因敲除稳定细胞株

利用CRISPR/Cas9基因编辑技术构建大鼠L2细胞α-ENaC基因敲除的细胞株,研究α-ENaC基因对细胞增殖的影响。构建敲除α-ENaC基因的CRISPR/Cas9表达载体和筛选报告载体,通过转染和嘌呤霉素筛选获得单克隆细胞株,Western Blot、测序确定突变的细胞株,CCK-8检测突变细胞株的增殖活力。成功构建靶向α-ENaC基因第一外显子的CRISPR/Cas9表达载体和筛选报告载体,嘌呤霉素筛选后,挑选8个单细胞克隆中有两个单细胞克隆α-ENaC蛋白表达下降,一个单细胞克隆α-ENaC蛋白不再表达,测序结果显示3个单细胞克隆分别为2个单等位基因突变和1个双等位基因突变,且未发现脱靶现象。突变细胞株的增殖活力降低,其中双等位基因突变细胞株增殖活力降低更为显著。因此,利用CRISPR/Cas9结合SSA-RPG报告载体成功获得了α-ENaC基因敲除的L2细胞株,α-ENaC与细胞增殖有关。     

敲除ESR1基因对人乳腺癌细胞侵袭能力的影响

目的:建立CRISPR/Cas9系统用于敲除人源雌激素受体α(ERα)基因(ESR1),并利用此细胞模型初步检测ESR1基因对乳腺癌细胞侵袭能力的影响。方法:设计一个靶向人源ESR1基因第2外显子的单向导RNA(sg RNA),分别克隆表达载体后,通过慢病毒转入人乳腺癌细胞株MCF-7,Western印迹检测MCF-7中ESR1基因的敲除效果,通过Transwell、反向侵袭试验观察ESR1基因敲除后对细胞侵袭能力的影响。结果:测序结果显示靶向ESR1基因CRISPR/Cas9重组质粒构建成功;Western印迹显示Cas9-ERα组的MCF-7细胞内ERα表达水平较对照组显著降低;Tanswell、反向侵袭试验证实ESR1基因敲除能够促进乳腺癌细胞的侵袭能力。结论:通过CRISPR/Cas9系统获得了靶向ESR1基因的重组质粒,构建的重组质粒能有效敲除ESR1基因;ERα能够抑制乳腺癌细胞的侵袭能力。     

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis,tobacco, sorghum and rice

The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-fuctional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites in its 5′ coding regions that were successfully cleaved by a CAS9/sgRNA complex that, along with error-prone DNA repair, resulted in creation of functional GFP genes. DNA sequencing confirmed Cas9/sgRNA-mediated mutagenesis at the target site. Rice protoplast cells transformed with Cas9/sgRNA constructs targeting the promoter region of the bacterial blight susceptibility genes, OsSWEET14 and OsSWEET11, were confirmed by DNA sequencing to contain mutated DNA sequences at the target sites. Successful demonstration of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.     

Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish

Customized TALENs and Cas9/gRNAs have been used for targeted mutagenesis in zebrafish to induce indels into protein-coding genes. However, indels are usually not sufficient to disrupt the function of non-coding genes, gene clusters or regulatory sequences, whereas large genomic deletions or inversions are more desirable for this purpose. By injecting two pairs of TALEN mRNAs or two gRNAs together with Cas9 mRNA targeting distal DNA sites of the same chromosome, we obtained predictable genomic deletions or inversions with sizes ranging from several hundred bases to nearly 1 Mb. We have successfully achieved this type of modifications for 11 chromosomal loci by TALENs and 2 by Cas9/gRNAs with different combinations of gRNA pairs, including clusters of miRNA and protein-coding genes. Seven of eight TALEN-targeted lines transmitted the deletions and one transmitted the inversion through germ line. Our findings indicate that both TALENs and Cas9/gRNAs can be used as an efficient tool to engineer genomes to achieve large deletions or inversions, including fragments covering multiple genes and non-coding sequences. To facilitate the analyses and application of existing ZFN, TALEN and CRISPR/Cas data, we have updated our EENdb database to provide a chromosomal view of all reported engineered endonucleases targeting human and zebrafish genomes.     

应用CRISPR/Cas9技术在杨树中高效敲除多个靶基因

CRISPR/Cas9系统是一种广泛应用于细菌、酵母、动物和植物中的基因组定点编辑技术。本课题组在前期工作中利用该系统在毛白杨(Populus tomentosa Carr.)中率先实现了对内源基因—八氢番茄红素脱氢酶(Phytoene dehydrogenase, PDS)基因的定点敲除。为研究靶点的设计和选择对该系统介导的杨树内源基因敲除效率的影响,本文分析了不同单向导RNA(Single-guide RNA, sgRNA)结合毛白杨PDS(PtPDS)靶基因DNA序列后对突变效率的影响。结果发现sgRNA与靶基因间的碱基错配会导致突变的效率降低,甚至不能突变,其中3′端的碱基配对更为重要。进一步测序分析发现,该系统能同时敲除杨树基因组上两个同源的PDS编码基因(PtPDS1和PtPDS2),突变率分别达86.4%和50%。研究证明该系统可快速高效地敲除两个以上的内源基因,获得多重突变体杨树株系。利用该技术,本课题组已获得多个杨树转录因子及结构基因的敲除突变体株系,为将来开展基因功能研究和杨树遗传改良奠定了基础。     

Efficient generation of zebrafish maternal-zygotic mutants through transplantation of ectopically induced and Cas9/gRNA targeted primordial germ cells

The clustered regularly interspaced short palindromic repeats(CRISPR)/Cas9 technology has been widely utilized for knocking out genes involved in various biological processes in zebrafish. Despite this technology is efficient for generating different mutations, one of the main drawbacks is low survival rate during embryogenesis when knocking out some embryonic lethal genes. To overcome this problem, we developed a novel strategy using a combination of CRISPR/Cas9 mediated gene knockout with primordial germ cell(PGC) transplantation(PGCT) to facilitate and speed up the process of zebrafish mutant generation, particularly for embryonic lethal genes. Firstly, we optimized the procedure for CRISPR/Cas9 targeted PGCT by increasing the efficiencies of genome mutation in PGCs and induction of PGC fates in donor embryos for PGCT. Secondly, the optimized CRISPR/Cas9 targeted PGCT was utilized for generation of maternal-zygotic(MZ) mutants of tcf7l1a(gene essential for head development), pou5f3(gene essential for zygotic genome activation) and chd(gene essential for dorsal development) at F_1 generation with relatively high efficiency. Finally, we revealed some novel phenotypes in MZ mutants of tcf7l1 a and chd, as MZtcf7l1 a showed elevated neural crest development while MZchd had much severer ventralization than its zygotic counterparts. Therefore, this study presents an efficient and powerful method for generating MZ mutants of embryonic lethal genes in zebrafish. It is also feasible to speed up the genome editing in commercial fishes by utilizing a similar approach by surrogate production of CRISPR/Cas9 targeted germ cells.     

Efficient Gene Knockout in Goats Using CRISPR/Cas9 System

The CRISPR/Cas9 system has been adapted as an efficient genome editing tool in laboratory animals such as mice, rats, zebrafish and pigs. Here, we report that CRISPR/Cas9 mediated approach can efficiently induce monoallelic and biallelic gene knockout in goat primary fibroblasts. Four genes were disrupted simultaneously in goat fibroblasts by CRISPR/Cas9-mediated genome editing. The single-gene knockout fibroblasts were successfully used for somatic cell nuclear transfer (SCNT) and resulted in live-born goats harboring biallelic mutations. The CRISPR/Cas9 system represents a highly effective and facile platform for targeted editing of large animal genomes, which can be broadly applied to both biomedical and agricultural applications.     

Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs

The CRISPR/Cas9 system has been implemented in a variety of model organisms to mediate site-directed mutagenesis. A wide range of mutation rates has been reported, but at a limited number of genomic target sites. To uncover the rules that govern effective Cas9-mediated mutagenesis in zebrafish, we targeted over a hundred genomic loci for mutagenesis using a streamlined and cloning-free method. We generated mutations in 85% of target genes with mutation rates varying across several orders of magnitude, and identified sequence composition rules that influence mutagenesis. We increased rates of mutagenesis by implementing several novel approaches. The activities of poor or unsuccessful single-guide RNAs (sgRNAs) initiating with a 5′ adenine were improved by rescuing 5′ end homogeneity of the sgRNA. In some cases, direct injection of Cas9 protein/sgRNA complex further increased mutagenic activity. We also observed that low diversity of mutant alleles led to repeated failure to obtain frame-shift mutations. This limitation was overcome by knock-in of a stop codon cassette that ensured coding frame truncation. Our improved methods and detailed protocols make Cas9-mediated mutagenesis an attractive approach for labs of all sizes.     

斑马鱼tbx2b调控心脏房室间隔发育的功能研究*

tbx2是早期心脏发育的关键基因。为进一步探究其对房室间隔(AVC)发育的影响,研究利用CRISPR/Cas9介导的基因敲除技术,成功构建了斑马鱼tbx2b突变体。通过T7E1酶切对其F₀进行敲除效率检测,结果显示平均敲除效率约为57.5%。F₁进一步筛选获得tbx2b杂合突变体,测序结果显示突变类型为11 bp碱基缺失的移码突变。tbx2b杂合子内交获得纯合子,tbx2b纯合突变体在5 dpf死亡并出现早期心脏环化异常表型。斑马鱼整胚原位杂交实验显示在3 dpf tbx2b纯合突变体中, 心脏腔室分化特异性标志基因nppa、nppb表达上调并异位表达在AVC,而AVC发育关键基因has2的表达消失。高效构建tbx2b突变体并初探其对下游基因的影响,为后续深入研究tbx2b对心脏AVC发育的作用奠定了基础,同时加深了人们对早期心脏调控网络的认识。