large-scale construction of uas-cdna/orf plasmids by crispr-based modular assembly (crisprmass)

CRISPRmass를 사용한 고처리량 UAS-cDNA/ORF 플라스미드 라이브러리 구축

Unbiased whole-genome genetic screening is a powerful approach for identifying genes involved in a given biological process and elucidating its mechanism. Therefore, it is widely used in various fields of biological research. Approximately 60% of Drosophila genes are conserved in humans1,2, and ~75% of human disease genes have homologs in Drosophila3. Genetic screening is mainly divided into two types: loss of function (LOF) and gain of function (GOF). LOF genetic screens in Drosophila have played a critical role in elucidating mechanisms that govern nearly every aspect of biology. However, the majority of Drosophila genes do not have obvious LOF phenotypes4, and therefore, GOF screening is an important method for studying the function of those genes4,5.
The binary GAL4/UAS system is commonly used for tissue-specific gene expression in Drosophila6. In this system, the tissue specifically expresses yeast transcription activator GAL4 that binds to the GAL4 responsive element (UAS) and thereby activates transcription of the downstream genetic components (e.g., cDNA and ORF)6. To perform genome-wide GOF screens in Drosophila, we need to construct a genome-wide UAS-cDNA/ORF plasmid library and, subsequently, a transgenic UAS-cDNA/ORF library in Drosophila.
Construction of a genome-wide UAS-cDNA/ORF plasmid library by conventional methods from publicly available cDNA/ORF clones is time-consuming and laborious, as every gene requires individualized designs, including primer design and synthesis, polymerase chain reaction (PCR), and gel purification, sequencing, restriction digestion, and so on7,8. Therefore, the construction of such a plasmid library is a rate-limiting step in creating a genome-wide transgenic UAS-cDNA/ORF library in Drosophila. Recently, we successfully solved this problem by developing a novel method, CRISPR-based modular assembly (CRISPRmass)9. The core of CRISPRmass is to manipulate the shared vector sequences of a plasmid library through a combination of gene editing technology and seamless cloning technology.
Here, we present a protocol for CRISPRmass, which includes massively parallel two-step test tube reactions followed by bacterial transformation. CRISPRmass is a simple, fast, efficient, and cost-effective method that, in principle, can be used for high-throughput construction of various plasmid libraries.
CRISPRmass strategy 
The procedure of CRISPRmass starts with parallel two-step test tube reactions prior to Escherichia coli (E. coli) transformation (Figure 1). Step 1 is the cleavage of the identical vector backbones of the cDNA/ORF plasmids by Cas9/sgRNA. An ideal cleavage site is adjacent to the 5&#8242; end of cDNA/ORF. The cleavage products do not have to be purified. Step 2 is the insertion of a vector-specific UAS module into the Cas9/sgRNA linearized cDNA/ORF plasmids by Gibson assembly (hereafter referred to as single step reaction), resulting in UAS-cDNA/ORF plasmids. The 5&#8242; and 3&#8242; terminal sequences of a UAS module overlap with those of the linearized cDNA/ORF plasmids, enabling the single step reaction.
The single step reaction products are directly subjected to E. coli transformation. Theoretically, only the desired UAS-cDNA/ORF colonies can grow on Luria-Bertani (LB) plates that contain selection antibiotics corresponding to the antibiotic resistance gene of the UAS module. The UAS module is composed of a core UAS module, an antibiotic resistance gene distinct from that of cDNA or ORF plasmids, and the 5&#8242; and 3&#8242; terminal sequences. A core UAS module comprises 10 copies of UAS, an Hsp70 minimal promoter, an attB sequence for phiC31-mediated genomic integration, and a mini-white transformation marker for Drosophila7.

저자 스포트라이트: Simplifying Genome-Wide Plasmid Library Construction Using CRISPRmass

UAS-cDNA/ORF Plasmid Library의 고처리량 구축을 위한 CRISPR-based Modular Assembly

Functional genomic screening offers a powerful approach to probe gene function, and relies on the construction of genome-wide plasmid libraries. Conventional approaches for plasmid library construction are time-consuming and laborious. To address this question, we develop a simple and efficient method, CRISPR-based modular assembly, or CRISPRmass.Through cleavage of shared vector sequences of cDNA or ORF plasmid by CRISPR/Cas9 and subsequent insertion of UAS modules by adjacent assembly, the procedure of construction of a genome-wide plasmid library by CRISPRmass is standardized as massively parallel two-step test tube reactions before bacterial transformation. CRISPRmass allows the simple, fast, efficient, and cost-effective construction of various plasmid libraries. It can also be applied to editing various genome-wide plasmid libraries in general, and it's an alternative to gateway technology in high-throughput plasmid library editing, paving the way for the global studies of biological networks.

CRISPR-based Modular Assembly(CRISPRmass)에 의한 UAS-cDNA/ORF 플라스미드의 대규모 구축

CRISPR 기반 모듈러 어셈블리 또는 CRISPRmass의 병렬 2단계 시험관 반응을 수행하려면 시험관 반응 1단계에서 Cas9 sgRNA에 의해 cDNA/ORF 플라스미드의 동일한 벡터 백본을 절단합니다. 이렇게하려면 얼음 위의 알루미늄 냉각 블록에 적절하게 표시된 0.2 밀리리터 튜브를 배열하십시오. 적절한 양의 Cas9, sgRNA, Cas9 완충액 및 DEPC 처리수를 혼합하여 N회 반응에 대비한 마스터 믹스를 준비합니다.마스터 믹스의 구성 요소가 함께 추가되면 적절한 혼합을 보장하기 위해 동일한 와류를 발생시킵니다. 그런 다음 혼합물을 스핀 다운하고 마스터 혼합물 2 마이크로 리터를 각 0.2 밀리리터 튜브에 분주합니다. 다음으로, 각 튜브에 0.4 마이크로리터의 0.019 마이크로몰 cDNA/ORF 플라스미드를 추가합니다.섭씨 37도에서 1시간 동안 분열 반응을 배양합니다. 다음 시험관 반응, 2단계에서는 벡터 특이적 UAS 모듈을 결과 Cas9 선형화된 cDNA/ORF 플라스미드에 삽입합니다. 각 샘플에 대해 1.4 마이크로리터 단일 단계 반응을 설정하려면 라벨이 부착된 0.2 밀리리터 튜브를 얼음 위의 알루미늄 냉각 블록에 배열합니다.적절한 양의 UAS 모듈과 단일 단계 반응 어셈블리 마스터 믹스를 혼합하여 N개의 반응에 대한 마스터 믹스를 준비합니다. 스핀다운하기 전에 혼합물을 잘 소용돌이치십시오. 그런 다음 마스터 혼합물 0.77 마이크로 리터를 각 튜브에 분취합니다.각 튜브의 부분 표본에 0.7 마이크로리터의 Cas9 선형화된 cDNA/ORF 플라스미드를 추가하고 섭씨 50도에서 1시간 동안 반응을 배양합니다.

large-scale-construction-uas-cdnaorf-plasmids-crispr-based-modular

Research

JoVE Journal

Genetics

Large-Scale Construction of UAS-cDNA/ORF Plasmids by CRISPR-Based Modular Assembly (CRISPRmass)

CRISPR-Based Modular Assembly for High-Throughput Construction of a UAS-cDNA/ORF Plasmid Library

Functional genomics screening offers a powerful approach to probe gene function and relies on the construction of genome-wide plasmid libraries. Conventional approaches for plasmid library construction are time-consuming and laborious. Therefore, we recently developed a simple and efficient method, CRISPR-based modular assembly (CRISPRmass), for high-throughput construction of a genome-wide upstream activating sequence-complementary DNA/open reading frame (UAS-cDNA/ORF) plasmid library. Here, we present a protocol for CRISPRmass, taking as an example the construction of a GAL4/UAS-based UAS-cDNA/ORF plasmid library. The protocol includes massively parallel two-step test tube reactions followed by bacterial transformation. The first step is to linearize the existing complementary DNA (cDNA) or open reading frame (ORF) cDNA or ORF library plasmids by cutting the shared upstream vector sequences adjacent to the 5&#39; end of cDNAs or ORFs using CRISPR/Cas9 together with single guide RNA (sgRNA), and the second step is to insert a UAS module into the linearized cDNA or ORF plasmids using a single step reaction. CRISPRmass allows the simple, fast, efficient, and cost-effective construction of various plasmid libraries. The UAS-cDNA/ORF plasmid library can be utilized for gain-of-function screening in cultured cells and for constructing a genome-wide transgenic UAS-cDNA/ORF library in Drosophila.&#160;

We present a protocol for CRISPR-based modular assembly (CRISPRmass), a method for high-throughput construction of UAS-cDNA/ORF plasmid library in Drosophila using publicly available cDNA/ORF resources. CRISPRmass can be applied to editing various plasmid libraries.

Functional genomics screening offers a powerful approach to probe gene function and relies on the construction of genome-wide plasmid libraries. ...

연구

유전학

Large-Scale Transformation of UAS-cDNA/ORF Plasmids from CRISPR-Based Modular Assembly into E. coli

To transform the UAS cDNA/ORF plasmids products obtained from the CRISPR based modular assembly into Escherichia coli, pre-chill 10 microliter tips at four degrees Celsius. Also, pre-chill 1.5 milliliter tubes in an aluminum cooling block on ice. After thawing competent E.coli cells on ice for five minutes, add an aliquot of 10 microliters of the cells to each pre-chilled 1.5-milliliter tube.Then add one microliter of the UAS cDNA/ORF plasmid products to each tube containing 10 microliters of competent cells. Swirl the tube gently to mix and place it on ice for 30 minutes. Incubate the tubes at 42 degrees Celsius in a water bath for one minute.Then immediately chill on ice for two minutes. Add 100 microliters of SOC medium, prewarmed to 37 degrees Celsius, to each tube at room temperature and incubate the tubes in a shaking incubator at 250 RPM and 37 degrees Celsius for one hour. Next, warm the LB plates containing an antibiotic corresponding to the UAS module's antibiotic resistance gene to 37 degrees Celsius.Spread the cells onto the warm plates and incubate them at 37 degrees Celsius overnight.