Studies on the temporal,structural,and interacting features of the clubroot resistance gene Rcr1 using CRISPR/Cas9-based systems

Clubroot disease is a severe threat to Brassica crops globally,particularly in western Canada.Genetic resistance,achieved through pyramiding clubroot resistance(CR)genes with different modes of action,is the most important strategy for managing the disease.However,studies on the CR gene functions are quite limited.In this study,we have conducted investigations into the temporal,structural,and interacting features of a newly cloned CR gene,Rcr1,using CRISPR/Cas9 technology.For temporal functionality,we developed a novel CRISPR/Cas9-based binary vector,pHHIGR-Hsp18.2,to deliver Rcr1 into a susceptible canola line(DH12075)and observed that early expression of Rcr1 is critical for conferring resistance.For structural functionality,several independent mutations in specific domains of Rcr1 resulted in loss-offunction,highlighting their importance for CR phenotype.In the study of the interacting features of Rcr1,a cysteine protease gene and its homologous allele in canola were successfully disrupted via CRISPR/Cas9 as an interacting component with Rcr1 protein,resulting in the conversion from clubroot resistant to susceptible in plants carrying intact Rcr1.These results indicated an indispensable role of these two cysteine proteases in Rcr1-mediated resistance response.This study,the first of its kind,provides valuable insights into the functionality of Rcr1.Further,the new vector p HHIGR-Hsp18.2 demonstrated an inducible feature on the removal of add-on traits,which should be useful for functional genomics and other similar research in brassica crops.

Efficient generation of targeted point mutations in the Brassica oleracea var.botrytis genome via a modified CRISPR/Cas9 system

In this study,we used the modified CRISPR/Cas9 system to produce targeted point mutations in cauliflower.Acetolactate synthase(ALS)and Centromere-specific histone H3 variant(CENH3)genes were selected as the base-editing targets and hypocotyls of cauliflower were used as explants.For ALS gene,a C-to-T conversion in the Pro182 codon(CCT)can alter the encoded amino acid,likely resulting in herbicide resistance,and a C-to-T mutation in the Leu133 codon(CTT)in the CENH3 gene may produce a haploid inducer.Results indicated that the transformation efficiency was 1.8%–4.5%and the mutation efficiencies for the ALS and CENH3 genes were approximately 22%and 87%,respectively.The ALS mutant cauliflower showed strong herbicide resistance,with possible immediate implications for broadleaf weed control in cauliflower fields.

Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures

Certain amino acids changes in the human Na^(+)/K^(+)-ATPase pump,ATPase Na^(+)/K^(+)transporting subunit alpha 1(ATP1A1),cause Charcot-Marie-Tooth disease type 2(CMT2)disease and refractory seizures.To develop in vivo models to study the role of Na^(+)/K^(+)-ATPase in these diseases,we modified the Drosophila gene homolog,Atpα,to mimic the human ATP1A1 gene mutations that cause CMT2.Mutations located within the helical linker region of human ATP1A1(I592T,A597T,P600T,and D601F)were simultaneously introduced into endogenous Drosophila Atpαby CRISPR/Cas9-mediated genome editing,generating the Atpα^(TTTF)model.In addition,the same strategy was used to generate the corresponding single point mutations in flies(Atpα^(I571T),Atpα^(A576T),Atpα^(P579T),and Atpα^(D580F)).Moreover,a deletion mutation(Atpα^(mut))that causes premature termination of translation was generated as a positive control.Of these alleles,we found two that could be maintained as homozygotes(Atpα^(I571T)and Atpα^(P579T)).Three alleles(Atpα^(A576T),Atpα^(P579)and Atpα^(D580F))can form heterozygotes with the Atpαmut allele.We found that the Atpαallele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila.Flies heterozygous for Atpα^(TTTF)mutations have motor performance defects,a reduced lifespan,seizures,and an abnormal neuronal morphology.These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.

Conversion of a normal maize hybrid into a waxy version using in vivo CRISPR/Cas9 targeted mutation activity

Waxy maize is a specialty maize that produces mainly amylopectin starch with special food or industrial values. The objective of this study was to overcome the limitations of wx mutant allele acquisition and breeding efficiency by conversion of parental lines from normal to waxy maize. The intended mutation activity was achieved by in vivo CRISPR/Cas9 machinery involving desired-target mutation of the Wx locus in the ZC01 background,abbreviated as ZC01-DTM^(wx). Triple selection was applied to segregants to obtain high genome background recovery with transgene-free wx mutations. The targeted mutation was identified, yielding six types of mutations among progeny crossed with ZC01-DTM^(wx).The amylopectin contents of the endosperm starch in mutant lines and hybrids averaged94.9%, while those of the wild-type controls were significantly(P < 0.01) lower, with an average of 76.9%. Double selection in transgene-free lines was applied using the Bar strip test and Cas9 PCR screening. The genome background recovery ratios of the lines were determined using genome-wide SNP data. That of lines used as male parents was as high as98.19% and that of lines used as female parents was as high as 86.78%. Conversion hybrids and both parental lines showed agronomic performance similar to that of their wild-type counterparts. This study provides a practical example of the efficient extension of CRISPR/Cas9 targeted mutation to industrial hybrids for transformation of a recalcitrant species.

CRISPR/Cas9 technology and its application in horticultural crops

Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated 9(CRISPR/Cas9)system has recently become one popular technology due to its efficiency,precision,and simplicity compared with other genome editing tools such as Zinc Finger Nucleases(ZFNs)and Transcription Activator Like Effector Nucleases(TALENs).Horticultural crops provide energy and health-keeping nutrients to humankind.Genome-editing technology has become widely adopted in horticultural breeding with the increasing demand for high yield and better-quality horticultural crops.Here,we describe the CRISPR/Cas9 system construction,its optimization,including sgRNA promoter,sgRNA design,Cas9 protein promoter,SpCas9 variants and orthologs,and vector delivery methods.We also summarized the application of this technology in horticultural plants for stress responses enhancement,fruit quality improvement,and cultivation traits modification.This detailed review was compiled to help establish comprehensive understanding of the CRISPR/Cas9 systems and provide a reference for further developing this technology to manipulate horticultural plant traits effectively.

Genetic mutation of Tas2r104/Tas2r105/Tas2r114 cluster leads to a loss of taste perception to denatonium benzoate and cucurbitacin B

Background:Bitter taste receptors(Tas2rs)are generally considered to sense various bitter compounds to escape the intake of toxic substances.Bitter taste receptors have been found to widely express in extraoral tissues and have important physiological functions outside the gustatory system in vivo.Methods:To investigate the physiological functions of the bitter taste receptor cluster Tas2r106/Tas2r104/Tas2r105/Tas2r114 in lingual and extraoral tissues,multiple Tas2rs mutant mice and Gnat3 were produced using CRISPR/Cas9 gene-editing technique.A mixture containing Cas9 and sgRNA mRNAs for Tas2rs and Gnat3 gene was microinjected into the cytoplasm of the zygotes.Then,T7EN1 assays and sequencing were used to screen genetic mutation at the target sites in founder mice.Quantitative real-time polymerase chain reaction(qRT-PCR)and immunostaining were used to study the expression level of taste signaling cascade and bitter taste receptor in taste buds.Perception to taste substance was also studied using twobottle preference tests.Results:We successfully produced several Tas2rs and Gnat3 mutant mice using the CRISPR/Cas9 technique.Immunostaining results showed that the expression of GNAT3 and PLCB2 was not altered in Tas2rs mutant mice.But qRT-PCR results revealed the changed expression profile of m Tas2rs gene in taste buds of these mutant mice.With two-bottle preference tests,these mutant mice eliminate responses to cycloheximide due to genetic mutation of Tas2r105.In addition,these mutant mice showed a loss of taste perception to quinine dihydrochloride,denatonium benzoate,and cucurbitacin B(CuB).Gnat3-mediated taste receptor and its signal pathway contribute to CuB perception.Conclusions:These findings implied that these mutant mice would be a valuable means to understand the biological functions of TAS2Rs in extraoral tissues and investigate bitter compound-induced responses mediated by these TAS2Rs in many extraoral tissues.

运用CRISPR/Cas9技术构建PCSK9点突变家兔模型

目的:运用CRISPR/Cas9基因编辑技术构建前蛋白转化酶枯草溶菌素9(PCSK9)点突变家兔模型。方法:根据Pub Med基因蛋白数据对人和兔的PCSK9蛋白功能区进行Blast分析,发现人PCSK9基因的386S(丝氨酸)氨基酸功能区与兔PCSK9基因的485S同源。根据家兔PCSK9基因的485S对应的碱基替换位置及序列分析结果设计3条单链向导RNA和1条单链寡核苷酸供体模板。将合成的单链向导RNA、Cas9 m RNA和单链寡核苷酸供体共同注射入家兔受精卵细胞质内并将胚胎移植入待孕母兔体内。对获得的F0代兔进行PCR、TA克隆、脱靶检测以鉴定PCSK9S386A是否突变成功。利用获得的PCSK9S386A基因点突变家兔进行繁殖,扩大群体。结果:共获得15只F0代兔,其中1只为PCSK9S386A点突变纯合子,2只为PCSK9S386A点突变杂合子,且该突变可以稳定遗传。结论:利用CRISPR/Cas9技术成功构建了PCSK9S386A点突变家兔模型,为探究PCSK9功能减弱的分子机制,开发可靠、有效的诊断和治疗措施提供了良好的动物模型。

CRISPR／Cas9系统在现代生物学研究和临床试验中的应用

规律成簇间隔短回文重复结构(clustered regularly interspaced short palindromic repeats,CRISPR)/CRISPR相关蛋白9(CRISPR-associated protien 9,Cas9)系统在生物医学研究中被广泛应用于基因编辑及探索基因的功能。这种基因编辑技术越来越多地运用在人类疾病的治疗中,包括巴斯综合征、杜氏肌萎缩症、血友病、地中海贫血和囊性纤维化。CRISPR/Cas 9基因编辑系统可以在体外细胞实验和体内动物实验上修复突变的DNA序列,也能改变CCR5、PD-1/L1、CAR-T等基因序列,用于控制HIV病毒的入侵及提高肿瘤免疫治疗的疗效。该技术还被运用于诱导多能干细胞(induced pluripotent stem cells,iPS)分化,形成某些具有功能的器官用于器官移植。本文综述了CRISPR/Cas 9系统的来源、结构和作用原理,以及其在现代生物学研究和基因治疗领域的应用。

Comparing successful gene knock-in efficiencies of CRISPR/Cas9 with ZFNs and TALENs gene editing systems in bovine and dairy goat fetal fibroblasts

This study aimed to compare the efficiencies of clustered regulatory interspaced short palindromic repeat（CRISPR）/Cas9-mediated gene knock-ins with zinc finger nucleases（ZFNs） and transcription activator-like effector nucleases（TALENs） in bovine and dairy goat fetal fibroblasts. To test the knock-in efficiency, a set of ZFNs and CRISPR/Cas9 plasmids were designed to edit the bovine myostatin（MSTN） gene at exon 2, while a set of TALENs and CRISPR/Cas9 plasmids were designed for editing the dairy goat β-casein gene at exon 2. Donor plasmids utilizing the ZFNs, TALENs, and CRISPR/Cas9 cutting sites were constructed in theGFP-PGK-Neo R plasmid background, including a 5′ and 3′ homologous arm flanking the genes humanized Fat-1（h Fat-1） or enhanced green fluorescent protein（eGFP）. Subsequently, the ZFNs, TALENs, or CRISPR/Cas9 and thehFat-1 or eGFP plasmids were co-transfected by electroporation into bovine and dairy goat fetal fibroblasts. After G418（Geneticin） selection, single cells were obtained by mouth pipetting, flow cytometry or a cell shove. The gene knock-in events were screened by PCR across the homologous arms. The results showed that in bovine fetal fibrobalsts, the efficiencies of ZFNs-mediated eGFP andhFat-1 gene knock-ins were 13.68 and 0%, respectively. The efficiencies of CRISPR/Cas9-mediated eGFP andhFat-1 gene knock-ins were 77.02 and 79.01%, respectively. The eGFP gene knock-in efficiency using CRISPR/Cas9 was about 5.6 times higher than when using the ZFNs gene editing system. Additionally, thehFat-1 gene knock-in was only obtained when using the CRISPR/Cas9 system. The difference of knockin efficiencies between the ZFNs and CRISPR/Cas9 systems were extremely significant（P〈0.01）. In the dairy goat fetal fibroblasts, the efficiencies of TALENs-mediated eGFP andhFat-1 gene knock-ins were 32.35 and 26.47%, respectively. Theefficiencies of eGFP and hFat-1 gene knock-ins using CRISPR/Cas9 were 70.37 and 74.29%, respectively. The knock-in efficiencies difference between the TALENs and CRISPR/Cas9 systems were extremely significant（P〈0.01）. This study demonstrated that CRISPR/Cas9 was more efficient at gene knock-ins in domesticated animal cells than ZFNs and TALENs. The CRISPR/Cas9 technology offers a new era of precise gene editing in domesticated animal cell lines.

CRISPR/Cas9 system and its applications in nervous system diseases

The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)system is an acquired immune system of many bacteria and archaea,comprising CRISPR loci,Cas genes,and its associated proteins.This system can recognize exogenous DNA and utilize the Cas9 protein's nuclease activity to break DNA double-strand and to achieve base insertion or deletion by subsequent DNA repair.In recent years,multiple laboratory and clinical studies have revealed the therapeutic role of the CRISPR/Cas9 system in neurological diseases.This article reviews the CRISPR/Cas9-mediated gene editing technology and its potential for clinical application against neurological diseases.

Addressing challenges in the clinical applications associated with CRISPR/Cas9 technology and ethical questions to prevent its misuse

The recently developed RNA-guided clustered regularly interspaced short palindromic repeat （CRISPR）/CRISPR-associated 9 （Cas9） nuclease system has progressed to be an invaluable technology for genome manipulation in somatic cell types and germline model organisms. While the unprecedented advance in human embryo gene editing research has great potential in next-generation therapeutics, it raises various ethical concerns that need to be addressed before being translated for clinical use. Here, we discuss the current and potential applications of CRISPR/Cas9 technology and its limitations in clinical applications, as well as ethical and legal considerations in the treatment, disease prevention or disability in somatic cells or human embryo via gene editing.

Using a novel cellular platform to optimize CRISPR/CAS9 technology for the gene therapy of AIDS

Dear Editor,Despite tremendous effort devoted to the development of antiretroviral therapies to combat HIV over the past decades, AIDS remains one of the most important global infectious diseases. According to UNAIDS report on the global AIDS epidemic in 2016, the estimated number of people living with HIV rose from 7.5 million in 2010 to 36.7 million in 2015. Furthermore, drug-resistance HIV strains have recently been reported （Wensing et al., 2017）. Therefore, it is important to develop new therapies to eliminate HIV in the patients. Immortalized cell lines representing the major targets of HIV in human are important for HIV research and therapeutic development.

CRISPR/Cas核酸检测技术的研究进展

CRISPR(clustered regularly interspaced short palindromic repeats)技术作为强大的基因编辑及基因调控工具,在生命科学研究、生物技术产业、基因治疗等领域得到了广泛的发展与应用.近些年来,基于Cas蛋白(CRISPRassociated protein)特异性及非特异性的核酸切割活性,CRISPR技术在核酸检测领域展现了其简单快速、高效特异的特点,以及在即时检测(point-of-care testing,POCT)领域的应用潜能,可满足临床早期治疗及床旁监护所需的快速诊断需求.根据Cas酶的不同活性(顺式切割活性和反式切割活性),本文将基于Cas酶的核酸检测技术分为两大类,分别为CRISPR/Cas9系统和CRISPR/Cas12,Cas13,Cas14系统,并阐述了它们各自的工作原理.此外,本文还详细综述了CRISPR/Cas系统与多信号传感器的联合应用,总结了CRISPR/Cas核酸检测技术所存在的缺陷及面临的挑战,并对其未来的发展进行了展望.

Efficient BoPDS Gene Editing in Cabbage by the CRISPR/Cas9 System

Genome editing offers great advantages in identifying gene function and generating agronomically important mutations in crops. Here,we report that the genome of cabbage(Brassica oleracea var. capitata), an important cruciferous vegetable, can also be precisely edited by a CRISPR/Cas9 system stacked with multiple single-guide RNA-expressing cassettes. When the phytoene desaturase Bo PDS gene was used as the target gene, an albino-phenotype transgenic shoot in T0 Basta-resistant lines was observed, and 37.5% of the transgenic cabbage shoots carried Bo PDS gene mutations as a result of nucleotide deletions at the expected position. Moreover, mutations were detected in sites with the same target sequence in gene Bol016089 which is paralogous to the Bo PDS gene. Our results show that the CRISPR/Cas9 system is a powerful tool for cabbage variety improvement by genome editing.

Single-nucleotide editing for zebra3 and wsl5 phenotypes in rice using CRISPR/Cas9-mediated adenine base editors

The CRISPR/Cas9-mediated base editing technology can efficiently generate point mutations in the genome without introducing a double-strand break(DSB)or supplying a DNA donor template for homology-directed repair(HDR).In this study,adenine base editors(ABEs)were used for rapid generation of precise point mutations in two distinct genes,OsWSL5,and OsZEBRA3(Z3),in both rice protoplasts and regenerated plants.The precisely engineered point mutations were stably inherited to subsequent generations.These single nucleotide alterations resulted in single amino acid changes and associated wsl5 and z3 phenotypes as evidenced by white stripe leaf and light green/dark green leaf pattern,respectively.Through selfing and genetic segregation,transgene-free,base edited wsl5 and z3 mutants were obtained in a short period of time.We noticed a novel mutation(V540A)in Z3 locus could also mimic the phenotype of Z3 mutation(S542P).Furthermore,we observed unexpected non-A/G or T/C mutations in the ABE editing window in a few of the edited plants.The ABE vectors and the method from this study could be used to simultaneously generate point mutations in multiple target genes in a single transformation and serve as a useful base editing tool for crop improvement as well as basic studies in plant biology.

The Application of CRISPR-Cas9 Genome Editing in Caenorhabditis elegans

Genome editing using the Cas9 endonuclease of Streptococcus pyogenes has demonstrated unparalleled efficacy and facility for modifying genomes in a wide variety of organisms. Caenorhabditis elegans is one of the most convenient multicellular organisms for genetic analysis, and the application of this novel genome editing technique to this organism promises to revolutionize analysis of gene function in the future. CRISPR-Cas9 has been successfully used to generate imprecise insertions and deletions via non-homologous end-joining mechanisms and to create precise mutations by homology-directed repair from donor templates. Key variables are the methods used to deliver the Cas9 endonuclease and the efficiency of the single guide RNAs. CRISPR-Cas9-mediated editing appears to be highly specific in C. elegans, with no reported off-target effects. In this review, 1 briefly summarize recent progress in CRISPR-Cas9-based genome editing in C. elegans, highlighting technical improvements in mutagenesis and mutation detection, and discuss potential future appli- cations of this technique.

DRISPR/Cas9 Platforms for Genome Editing in Plants： Developments and Applications

The clustered regularly interspaced short palindromic repeat （CRISPR）-associated protein9 （Cas9） genome editing system （CRISPR/Casg） is adapted from the prokaryotic type II adaptive immunity system. The CRISPR/Cas9 tool surpasses other programmable nucleases, such as ZFNs and TALENs, for its simplicity and high efficiency. Various plant-specific CRISPR/Cas9 vector systems have been established for adap- tion of this technology to many plant species. In this review, we present an overview of current advances on applications of this technology in plants, emphasizing general considerations for establishment of CRISPR/ Cas9 vector platforms, strategies for multiplex editing, methods for analyzing the induced mutations, fac- tors affecting editing efficiency and specificity, and features of the induced mutations and applications of the CRISPR/Cas9 system in plants. In addition, we provide a perspective on the challenges of CRISPR/Cas9 technology and its significance for basic plant research and crop genetic improvement.

大豆NIN和NLP基因生物信息学分析及敲除载体构建

为促进大豆NLP家族基因突变大豆材料的获得及大豆NIN和NLP基因功能的研究,本研究对大豆NIN和NLP基因进行生物信息学分析,通过CRISPR/Cas 9基因编辑技术构建基因敲除载体,并且通过大豆毛根转化实验验证靶点的有效性。结果表明:大豆基因组中一共存在4个NIN基因和10个NLP基因家族成员,这些基因都具有RWP-RK和PB1两个保守结构域。亚细胞定位预测表明所有成员都定位在细胞核中,此外GmNIN1b和GmNIN2a还定位于叶绿体。GmNIN1a/b、GmNIN2a/b、GmNLP2a/b及GmNLP3b在根瘤中的表达量相对较高,推测这些基因可能对结瘤过程具有重要的调控功能。成功构建了NLP4和NLP5两个敲除载体,得到可敲除GmNLP4a/b的3个有效靶点和敲除GmNLP5a/b的2个有效靶点。本研究获得了大豆NIN和NLP基因家族的生物信息学依据和创制GmNLP4a/b和GmNLP5a/b基因突变体的技术依据。

盘状结构域受体1对实验性结肠炎小鼠肠道炎症及纤维化的影响

目的探究盘状结构域受体1(discoidin domain receptors,DDR1)在慢性结肠炎小鼠肠道炎症及肠纤维化中的功能。方法针对DDR1基因exon4设计并合成gRNA序列,与编码Cas9的mRNA混合显微注射入C57BL/6小鼠受精卵内,构建DDR1基因突变小鼠。选择F4代基因敲除纯合子小鼠(DDR1^(-/-))和野生型C57BL/6小鼠,通过葡聚糖硫酸钠(DSS)诱导慢性结肠炎模型。比较两组小鼠疾病活动指数(DAI)、体质量、结肠长度及组织病理学变化。ELISA法检测外周血细胞因子的含量,Western blot法检测小鼠结肠纤维化相关蛋白表达。结果PCR法检测结果显示利用CRISPR/Cas9技术成功构建DDR1^(-/-)小鼠;循环饮用DSS后,与野生型小鼠相比,DDR1^(-/-)小鼠体质量下降减缓,DAI评分及肠组织病理学评分降低,结肠短缩减轻(5.81±0.11 cm vs 5.19±0.05 cm,P<0.05);血清IL-1β、TNF-α及TGF-β水平下调(P<0.01);Masson染色胶原容积评分显示肠纤维化减轻(DSS-WT vs DSS-DDR1,41.43±0.08 cm vs 21.37±0.07 cm,P<0.01);肠组织TGF-β、α-SMA和COL1A1的蛋白表达下降。结论DDR1参与慢性结肠炎的发生,敲除DDR1基因可减轻慢性结肠炎肠道炎症及纤维化的症状和疾病进程。

Regulating CRISPR/Cas9 Using Streptavidin-Biotin Interactions

Comprehensive Summary Currently,CRISPR/Cas9 technology has found widespread applications across various domains.However,the utility of CRISPR/Cas9 is encumbered by issues pertaining to its reliability and safety,primarily stemming from the uncontrolled activity of the system.Therefore,the design and development of CRISPR/Cas9 systems with controllable activity is of paramount importance.Biotin,characterized by its small molecular weight,and streptavidin,distinguished by its substantial spatial steric hindrance,can be harnessed as an ideal OFF switch(termed a"bioactivity brake")due to their interaction characteristics.In this work,we present a strategy that employs the streptavidin-biotin interaction as a"brake system"for CRISPR/Cas9,effectively allowing for the shutdown of the enzymatic activity of CRISPR/Cas9.