CN105518137B - Method for specifically knocking out pig SALL1 gene by CRISPR-Cas9 and sgRNA for specifically targeting SALL1 gene - Google Patents
Method for specifically knocking out pig SALL1 gene by CRISPR-Cas9 and sgRNA for specifically targeting SALL1 gene Download PDFInfo
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Abstract
The invention discloses a method for specifically knocking out pig SALL1 gene by using CRISPR-Cas9 and sgRNA for specifically targeting SALL1 gene. The target sequence of sgRNA of the invention specifically targeting SALL1 gene on SALL1 gene conforms to the sequence arrangement rule of 5 '-N (20) NGG-3', wherein N (20) represents 20 consecutive bases, wherein each N represents a or T or C or G; the target sequence on SALL1 gene was located at the 3 exon coding region N-terminal to SALL1 gene or at the junction with the adjacent intron; the target sequence on the SALL1 gene is unique. The sgRNA disclosed by the invention is used in a method for specifically knocking out the pig SALL1 gene by CRISPR-Cas9, can quickly, accurately, efficiently and specifically knock out the pig SALL1 gene, and effectively solves the problems of long period and high cost in constructing SALL1 gene knock-out pigs.
Description
Technical Field
The invention relates to the technical field of genetic engineering, in particular to the technical field of gene knockout, and specifically relates to a method for specifically knocking out a pig SALL1 gene by using CRISPR-Cas9 and sgRNA for specifically targeting the SALL1 gene.
Background
Organ transplantation is the most effective treatment for organ failure. To date, nearly a million patients worldwide have continued their lives through organ transplantation. With the aging population and the advancement of medical technology, more and more patients need to undergo organ transplantation, but the shortage of donor organs severely restricts the development of organ transplantation. Taking kidney transplantation as an example, as many as 30 million patients need kidney transplantation every year in China, but no more than 1 million donor kidneys are available for transplantation, and most patients die of renal failure. The need for organ transplantation has not been met by means of post-mortem organ donation. The genetic engineering of other species to provide organs suitable for human transplantation has become a major approach to the problem of organ shortage in human donors.
At present, pigs become the most ideal source of xenogeneic organs according to the evaluation in many aspects such as biosafety, physiological function indexes, economy, rare species protection and the like. However, there is a great difference between pigs and humans, and a strong immune rejection reaction is generated by directly transplanting the organs of pigs to humans. Therefore, the genetic engineering of pigs to produce organs suitable for human transplantation is the ultimate goal of xenotransplantation.
The traditional technical route is to obtain a strain of swine that can be used for transplantation by reducing the differences in immunity between swine and humans. In recent years, the production of organs composed of human cells using organ development-deficient pigs as a culture environment has become a new idea. The gene for controlling the development of the pig organ is effectively interfered by genetic engineering, so that a certain organ of the pig is deleted in the development process, and a key culture environment is provided for the development of human cell organs.
The SALL1 gene is currently known to be an essential gene in kidney development. SALL1 has a homologous gene in drosophila, which is highly conserved evolutionarily. The SALL1 gene is expressed only during renal developmental stages, is histologically distributed to the metanephric mesenchymal cells and renal stroma, and is essential for entry of ureteric buds into the interstitial tissue. Deletion of the SALL1 gene resulted in neonatal rat renal hypoplasia or deletion, suggesting that SALL1 regulates key steps in the renal developmental process. The knockout of the SALL1 gene can ensure that the pig does not produce kidney in the development process, and provides a good development environment for human cell-derived kidney. The accurate and efficient knockout of the SALL1 gene of the pig is the first step.
Currently, common gene knockout technologies include Homologous Recombination (HR) technology, Transcription activation Effector-Like Nuclease (TALEN) technology, Zinc Finger Nuclease (ZFN) technology, and recently developed Regularly Clustered Short interspersed Palindromic Repeat (CRISPR) technology. HR technology is inefficient due to recombination (efficiency is only about 10)-6) The screening work for mutants is very time consuming and inefficient and has gradually been replaced. The cutting efficiency of the TALEN technology and the ZFN technology can generally reach 20%, but protein modules capable of identifying specific sequences need to be constructed, and the earlier work is complicated and time-consuming. The module design of the ZFN technology is complex and has high miss rate, and its application is limited.
CRISPR is an acquired immune system derived from prokaryotes, the complex that performs the interference function consisting of the protein Cas and CRISPR-rna (crrna). Three types of the system have been found, wherein the Cas9 system in the second type has simple composition and is actively applied to the field of genetic engineering. Cas9 targeted cleavage of DNA is achieved by the principle of complementary recognition of two small RNAs, crRNA (crispr RNA) and tracrRNA (trans-activating crRNA), to the target sequence. Two small RNAs have now been fused into one RNA strand, sgrna (single guide RNA) for short, capable of recognizing a specific gene sequence and guiding Cas9 protein cleavage. In eukaryotes, DNA is cleaved and end-linked by non-homologous recombination, resulting in frame shift mutations that ultimately result in functional gene knock-outs.
Compared with the 3 technologies, the CRISPR technology is simple to operate and high in screening efficiency, and can realize accurate targeted cutting. Therefore, the screening efficiency of SALL1 deleted cells and genetically engineered pigs with renal development deletion can be greatly improved by knocking out the SALL1 gene by the CRISPR technology. However, the key technical problem of the path is to design and prepare the sgRNA with accurate targeting, because the targeting accuracy of the gene is highly dependent on the sgRNA target sequence, and whether the sgRNA with accurate targeting can be successfully designed becomes the key technical problem of target gene knockout, and the invention aims to solve the technical problem so as to provide a solid foundation for knockout of the SALL1 gene.
Disclosure of Invention
The invention aims to provide a method for specifically knocking out pig SALL1 gene by CRISPR-Cas9 and sgRNA for specifically targeting SALL1 gene.
According to a first aspect of the invention, the invention provides sgrnas in CRISPR-Cas 9-specific knockout porcine SALL1 gene for specifically targeting SALL1 gene, the sgrnas having the following characteristics:
(1) the target sequence of the sgRNA on the SALL1 gene conforms to the sequence arrangement rule of 5 '-N (20) NGG-3', wherein N (20) represents 20 continuous bases, each N represents A or T or C or G, and the target sequence conforming to the rule is positioned on a sense strand or an antisense strand;
(2) the target sequence of the sgRNA on SALL1 gene is located in the 3 exon coding region at the N-terminus of SALL1 gene, or a portion of the target sequence is located in the 3 exons at the N-terminus of SALL1 gene, and the rest spans the boundary with the adjacent intron and is located in the adjacent intron;
(3) the sgRNA is unique in its target sequence on SALL1 gene.
As a preferred scheme of the invention, the target sequence is SEQ ID NO: 1 to 49 in sequence list.
As a preferred scheme of the invention, the target sequence is SEQ ID NO: 3 or 4.
According to a second aspect of the invention, the invention provides a method for specifically knocking out porcine SALL1 gene using CRISPR-Cas9, the method comprising the steps of:
(1) adding a sequence for forming a sticky end to the 5' -end of the target sequence of the sgRNA in the first aspect, and synthesizing to obtain a forward oligonucleotide sequence; adding appropriate sequences for forming cohesive ends to both ends of a complementary sequence corresponding to the target sequence of the sgRNA described in the first aspect, and synthesizing to obtain an inverted oligonucleotide sequence; annealing and renaturing the synthesized forward oligonucleotide sequence and the reverse oligonucleotide sequence to form double-stranded oligonucleotide with a sticky end;
(2) connecting the double-stranded oligonucleotide into a linearized expression vector carrying a Cas9 gene to obtain an expression vector carrying sgRNA oligonucleotide containing a corresponding target sequence and a Cas9 gene, transforming competent bacteria, screening and identifying correct positive clone, shaking the positive clone, and extracting a plasmid;
(3) packaging a pseudolentivirus simultaneously carrying sgRNA of a targeted SALL1 gene and Cas9 by using the expression vector, the packaging plasmid and the packaging cell line which carry the sgRNA oligonucleotide and the Cas9 gene;
(4) infecting a target cell with the pseudotyped lentivirus and further culturing; then collecting the infected target cell, amplifying a gene segment containing the target sequence by using the genome DNA of the infected target cell as a template, and determining the knockout condition of the SALL1 gene through denaturation, renaturation and enzyme digestion.
As a preferred scheme of the invention, the expression vector is SEQ ID NO: 50.
As a preferred embodiment of the present invention, the above method comprises the steps of:
(1) adding a CACCG sequence to the 5' -end of the target sequence of the sgRNA in the first aspect, and synthesizing to obtain a forward oligonucleotide sequence; adding an AAAC sequence to the 5 '-end and adding a C to the 3' -end of a complementary sequence corresponding to the target sequence of the sgRNA in the first aspect, and synthesizing to obtain a reverse oligonucleotide sequence; annealing and renaturing the synthesized forward oligonucleotide sequence and the reverse oligonucleotide sequence to form double-stranded oligonucleotide with a sticky end;
(2) the double-stranded oligonucleotide is connected into a nucleotide sequence shown as SEQ ID NO: 50, obtaining a linear vector by carrying out restriction enzyme digestion on an expression vector lentiCRISPR v2 with a sequence shown in 50 by BsmB I to obtain a recombinant expression vector lentiCRISPR v2-SALL1 carrying sgRNA oligonucleotide, transforming competent bacteria, screening and identifying correct positive clone, shaking the positive clone, and extracting plasmid;
(3) the expression vector lentiCRISPR v2-SALL1, a packaging plasmid and a packaging cell line are used for packaging a pseudolentivirus which simultaneously carries sgRNA of a targeting SALL1 gene and Cas 9;
(4) infecting a target cell by using the CRISPR pseudotyped slow virus and further culturing; then collecting the infected target cell, amplifying a gene segment containing the target sequence by using the genome DNA of the infected target cell as a template, and determining the knockout condition of the SALL1 gene through denaturation, renaturation and enzyme digestion.
As a preferred embodiment of the present invention, the above-mentioned packaging plasmids are plasmid pLP1, plasmid pLP2 and plasmid pLP/VSVG; the packaging cell line is HEK293T cell.
In a preferred embodiment of the present invention, the target cell is a porcine PIEC cell.
In a preferred embodiment of the present invention, the gene fragment including the target sequence is amplified using the genomic DNA as a template, and the knockout of the SALL1 gene is determined by denaturation, renaturation and enzyme digestion, specifically:
(a) amplifying a SALL1 gene fragment containing the target sequence of the sgRNA by using the upstream and downstream primers of the SALL1 gene and using the genomic DNA of a target cell infected with the virus as a template, and amplifying the genomic DNA of a wild-type cell not infected with the virus by using the same primers;
(b) purifying the amplified SALL1 gene fragment, and then heating and denaturing and renaturing the SALL1 gene fragment from the target cell infected with virus and the SALL1 gene fragment from the wild cell respectively to form hybrid DNA molecules;
(c) cutting the renatured hybrid DNA molecules by using Cruiser enzyme;
(d) and (3) detecting the enzyme digestion product by electrophoresis, and detecting the target sequence mediated SALL1 gene knockout effect.
According to a third aspect of the invention, the invention provides a recombinant expression vector lentiCRISPR v2-SALL1 used in a method for specifically knocking out porcine SALL1 gene by CRISPR-Cas9, wherein the sequence of a skeleton vector of the recombinant expression vector is shown as SEQ ID NO: 50 is shown; the carried target sequence is the target sequence of the sgRNA of the first aspect, preferably the sequence table SEQ ID NO: 3 or 4.
According to a fourth aspect of the invention, the invention provides the use of the sgRNA of the first aspect or the recombinant expression vector lentiCRISPR v2-SALL1 of the third aspect in a method of CRISPR-Cas9 specific knockout of porcine SALL1 gene.
The sgRNA of the specific targeting SALL1 gene is successfully found by aiming at CRISPR-Cas9 specific knockout of the pig SALL1 gene, and the application of the sgRNA in the method for CRISPR-Cas9 specific knockout of the pig SALL1 gene can quickly, accurately, efficiently and specifically knockout the pig SALL1 gene, and effectively solves the technical problems of long period and high cost in constructing SALL1 gene knockout pigs.
Drawings
Fig. 1 is a plasmid map of the vector plasmid lentiCRISPR v2 used in the examples of the present invention;
FIG. 2 is a plasmid map of the packaging plasmid pLP1 used in the examples of the present invention;
FIG. 3 is a plasmid map of the packaging plasmid pLP2 used in the examples of the present invention;
FIG. 4 is a plasmid map of the packaging plasmid pLP/VSVG used in the examples of the present invention;
FIG. 5 is a diagram showing the results of electrophoresis detection of the gene knockout effect of the enzyme digestion verification target sequence in the embodiment of the present invention, in which M represents DNA Marker, WT represents the results of Cruiser enzyme digestion detection of the PCR product of wild-type cells that have not undergone viral infection and Cas9 cleavage, 3 and 4 represent the targeted cleavage effect of the No. 3 and No. 4 target sequences on SALL1 gene in Table 1, respectively, and the arrow indicates small fragments obtained by cleavage with Cruiser enzyme.
Detailed Description
The technical solution of the present invention is further explained with reference to the accompanying drawings and specific embodiments. The drawings and the detailed description are not intended to limit the scope of the invention. Unless otherwise specified, the technical means used in the examples are conventional means well known to those skilled in the art, and the raw materials used are commercially available products.
Test materials and reagents referred to in the following examples: the lentiCRISPR v2 plasmids were purchased from addge corporation, the packaging plasmids pLP1, pLP2 and pLP/VSVG were purchased from Invitrogen corporation, the packaging cell line HEK293T cells were purchased from american type culture collection bank (ATCC), the PIEC cells were purchased from chinese academy of sciences cell bank, the DMEM medium, Opti-MEM medium and fetal bovine serum FBS were purchased from Gibco corporation, and the Lipofectamine2000 was purchased from Invitrogen corporation.
The molecular biological experiments, which are not specifically described in the following examples, were performed by referring to the specific methods described in molecular cloning, a laboratory manual (third edition) j. sambrook, or according to the kit and product instructions.
The general technical scheme of the invention comprises the following five parts:
selection and design of sgRNA target sequence of Sus scrofa (pig) SALL1 gene
sgRNA target sequence selection of SALL1 gene:
the appropriate 20bp oligonucleotide sequence was found in the exon region of SALL1 gene as the target sequence.
sgRNA target sequence design of SALL1 gene:
and (3) adding linkers to the target sequence and the complementary sequence to form a forward oligonucleotide sequence and a reverse oligonucleotide sequence.
Secondly, constructing CRISPR vector of SALL1 gene
1. The forward oligonucleotide sequence and the reverse oligonucleotide sequence are synthesized and renatured to form double-stranded DNA fragments (i.e., double-stranded target sequence oligonucleotides, which may also be referred to as double-stranded oligonucleotides) with sticky ends.
2. Constructing a CRISPR-sgRNA expression vector:
the double-stranded DNA fragment is constructed into a target vector (such as lentiCRISPR v2, and the plasmid map of the double-stranded DNA fragment is shown in figure 1) to form a lentivirus CRISPR vector such as lentiCRISPR v2-SALL 1.
Thirdly, obtaining the pseudotyped slow virus expressing SALL1sgRNA
A CRISPR pseudotyped lentivirus expressing SALL1sgRNA is produced by using a packaging plasmid, a packaging cell line and a lentivirus CRISPR vector.
Fourth, infecting target cells and detecting the knockout effect of SALL1 gene
1. Lentivirus infection of cells of interest:
pseudotyped lentiviruses such as lentiCRISPR v2-SALL1 were added to the cell culture medium of interest for infection and further culture.
2. Detecting the knockout effect of the SALL1 gene:
collecting target cells, amplifying a gene segment containing a target sequence by using genome DNA as a template, and determining the knockout condition of the SALL1 gene through denaturation, renaturation and enzyme digestion.
Fifthly, selecting and identifying SALL1 gene knockout monoclone
1. For a target cell group with a definite knockout effect, a plurality of cell strains with single cell sources are separated through dilution and monoclonal culture.
2. A monoclonal SALL1 knockout was identified.
The technical solution and the advantageous effects thereof of the present invention will be described in detail by examples below.
EXAMPLE I selection and design of sgRNA target sequence of Sus scrofa (pig) SALL1 Gene
The target sequence determines the targeting specificity of the sgRNA and the efficiency of inducing Cas9 to cleave the gene of interest. Therefore, efficient and specific target sequence selection and design are a prerequisite for constructing sgRNA expression vectors.
sgRNA target sequence selection of the SALL1 Gene
For the SALL1 gene, the following principles should be followed in the selection of target sequences:
(1) searching for a target sequence conforming to the 5 '-N (20) NGG-3' rule in the exon coding region of the SALL1 gene, wherein N (20) represents 20 consecutive bases, wherein each N represents A or T or C or G, and the target sequence conforming to the above rule is located in a sense strand or an antisense strand;
(2) selecting 3 exon coding regions sequences near the N-terminus, the target sequence may be the 3 exon coding regions located N-terminal to the SALL1 gene, or a portion of the target sequence may be the 3 exons located N-terminal to the SALL1 gene, with the remainder spanning the boundaries with the adjacent intron, located in the adjacent intron; cleavage of such coding region sequences would result in a functional knock-out of the SALL1 gene, leaving truncated sequences that would not form a functional protein;
(3) if multiple splice bodies exist, the coding region of the consensus exon is selected, and the sequence of the coding region of 3 exons near the N-terminal is selected for the SALL1 gene to meet the condition;
(4) the homology of the above target sequence in the porcine genome was analyzed using an online sequence analysis tool (http:// criprp. mit. edu /), the target sequences with significant homology were discarded and further selected according to the score, the selected target sequence being unique in the SALL1 gene.
Based on the above principle, the target sequence set shown in Table 1 was selected.
TABLE 1 set of target sequences
| Numbering | Sequence of |
| 1 | |
| 2 | |
| 3 | |
| 4 | GAGCGAGGCCACTTCGGGGT |
| 5 | GGGTCGGATTGGAAATGTTG |
| 6 | GCCTCGCTCCCCCGGCGAGA |
| 7 | CGGGGGAGCGAGGCCACTTC |
| 8 | CCGAAGTGGCCTCGCTCCCC |
| 9 | GGGGGAGCGAGGCCACTTCG |
| 10 | CCGGGGGAGCGAGGCCACTT |
| 11 | ACAGCACCGGCCGCAGACGT |
| 12 | CATTTGTTCATCGGGATGAT |
| 13 | TTGCTCTTAGTGGTGCGGTT |
| 14 | CATTTACGATTAAAACGAGT |
| 15 | CTTGCTCTTAGTGGTGCGGT |
| 16 | TCATTTGTTCATCGGGATGA |
| 17 | CAACCGCACCACTAAGAGCA |
| 18 | ATTTGTTCATCGGGATGATG |
| 19 | CACAGCACCGGCCGCAGACG |
| 20 | AGGATGCCCACGTCTGCGGC |
| 21 | GTGGGCATCCTTGCTCTTAG |
| 22 | CAAAGAACTCGGCACAGCAC |
| 23 | AGCAAGGATGCCCACGTCTG |
| 24 | CATCCTTGCTCTTAGTGGTG |
| 25 | TTTTCGTGCAGCTCTTCTTG |
| 26 | TTCATCGGGATGATGGGGAG |
| 27 | CGTGTCATTCATTTGTTCAT |
| 28 | ACGGTTAACAAAACAGAGCA |
| 29 | GGACTGGGGGAGAAGGGTTC |
| 30 | GCCGCCTTTGTTAGCCACCG |
| 31 | GAGGCCCCGGTGGCTAACAA |
| 32 | AGAACACCACGGGCCGGACA |
| 33 | TGCCGCCTTTGTTAGCCACC |
| 34 | CAGAACACCACGGGCCGGAC |
| 35 | GCCCCGGTGGCTAACAAAGG |
| 36 | CTGTCCGGCCCGTGGTGTTC |
| 37 | GTGGCTAACAAAGGCGGCAG |
| 38 | GCGACCTTCCAGAACACCAC |
| 39 | CCGGCCCGTGGTGTTCTGGA |
| 40 | ACTCTTCCCTGTCCGGCCCG |
| 41 | CCTTCCAGAACACCACGGGC |
| 42 | CTGCCGCCTTTGTTAGCCAC |
| 43 | TCCATGGACTCTTCCCTGTC |
| 44 | AGCGACCTTCCAGAACACCA |
| 45 | AAAGGCGGCAGTGGCCCCCT |
| 46 | GTGGCAGCAGCGATGGCAGT |
| 47 | GGACAGGGAAGAGTCCATGG |
| 48 | GCCGGACAGGGAAGAGTCCA |
| 49 | CAAAGGCGGCAGTGGCCCCC |
sgRNA target sequence design of SALL1 gene:
(1) a lentiCRISPR v2 plasmid is used as an expression vector, and a CACCG sequence is added to the 5' -end of the N (20) target sequence according to the characteristics of the lentiCRISPR v2 plasmid to form a forward oligonucleotide sequence:
5’-CACCGNNNNNNNNNNNNNNNNNNNN-3’；
(2) adding sequences to both ends of the reverse complement of the N (20) target sequence to form a reverse oligonucleotide sequence:
5’-AAACNNNNNNNNNNNNNNNNNNNNC-3’；
the forward oligonucleotide sequence and the reverse oligonucleotide sequence may be complementary to form a double-stranded DNA fragment with sticky ends:
5’-CACCGNNNNNNNNNNNNNNNNNNNN-3’
3’-CNNNNNNNNNNNNNNNNNNNNCAAA-5’。
example two construction of sgRNA expression vector for SALL1 Gene
1. Synthesis of DNA insert
(1) Synthesis of the designed Forward and reverse oligonucleotide sequences
Oligonucleotide sequences can be specifically synthesized by commercial companies (e.g., Invitrogen corporation) based on the sequences provided. The present example and the following examples investigated the effect of target sequences shown in sequence nos. 3 and 4 listed in table 1 on knockdown of SALL1 gene.
The forward and reverse oligonucleotide sequences corresponding to target sequence No. 3 are as follows:
CACCGTTTCCAATCCGACCCCGAAG(SEQ ID NO：51)；
AAACCTTCGGGGTCGGATTGGAAAC(SEQ ID NO：52)。
the forward and reverse oligonucleotide sequences corresponding to target sequence No. 4 are as follows:
CACCGGAGCGAGGCCACTTCGGGGT(SEQ ID NO：53)；
AAACACCCCGAAGTGGCCTCGCTCC(SEQ ID NO：54)。
the corresponding forward and reverse oligonucleotide sequences are annealed and renatured to form double-stranded DNA fragments having sticky ends.
The reaction system (20. mu.L) is shown below:
forward oligonucleotide (10. mu.M): 1 μ L
Reverse oligonucleotide (10 μ M): 1 μ L
10×PCR buffer：2μL
ddH2O：16μL
The reaction system was placed in a PCR apparatus and the reaction was carried out according to the following procedure.
Reaction procedure:
95℃,5min；
80℃,5min；
70℃,5min；
60℃,5min；
50℃,5min；
naturally cooling to room temperature.
2. Construction of sgRNA expression vector
(1) The BsmB I restriction enzyme is used for cutting the target vector lentiCRISPR v2 plasmid (the sequence of which is shown as SEQ ID NO: 50 in the sequence table).
The preparation method comprises the following steps:
the lentiscrispr v2 plasmid: 1 μ g
10 Xenzyme digestion buffer: 2 μ L
BsmB I restriction enzyme: 2 μ L
Supplemental ddH2O to a total volume of 20. mu.L
The enzyme digestion reaction system is placed at 37 ℃ for reaction for 4 h.
(2) Electrophoretic separation and purification of vector fragments
After completion of the digestion, the digestion mixture was separated by agarose gel electrophoresis, and the vector fragment (about 12kb) was selected for cleavage and recovered by a DNA gel recovery column.
(3) Connecting the synthesized double-stranded DNA fragment with the vector main fragment and transforming the double-stranded DNA fragment into escherichia coli
Performing ligation reaction on the double-stranded DNA fragment obtained by renaturation and the recovered vector fragment, and preparing according to the following reaction system:
the LentiCRISPR v2 vector fragment: 100ng
Double-stranded DNA fragment: 200ng
T4 ligase: 1 μ L
T4 ligation reaction buffer: 1 μ L
Supplemental ddH2O to a total volume of 10. mu.L
The ligation mixture was left to react for 2h at 25 ℃.
After the reaction was complete, the ligation mixture was transformed into E.coli strain DH5 α: add 100. mu.L E.coli DH 5. alpha. competent cells to the ligation mixture and incubate for 30min on ice; putting the mixture into a water bath at 42 ℃, performing heat shock for 90s, and then putting the mixture on ice for cooling; adding 100 μ L LB medium into the mixture, and shake culturing at 37 deg.C for 20 min; the mixture was spread on Amp LB plates and incubated at 37 ℃ for 14 h.
(4) Identification of the correct transformed clones
And selecting a plurality of colonies from the Amp LB plate for amplification culture, and extracting plasmids for enzyme digestion identification. Clones that are likely to be correct are selected for sequencing, and the correct insertion sequence is verified. The correct lentiCRISPR v2-SALL1 vector clone was used for seed preservation.
Example three obtaining a pseudotyped Lentivirus expressing SALL1sgRNA
1. Material preparation
The packaging plasmids pLP1, pLP2, and pLP/VSVG (purchased from Invitrogen, maps shown in FIG. 2, FIG. 3, and FIG. 4, respectively) were amplified and extracted; amplifying and extracting a vector plasmid lentiCRISPR v2-SALL 1; culturing packaging cell line HEK293T cells (purchased from ATCC); DMEM medium, Opti-MEM medium and fetal bovine serum FBS (purchased from Gibco); lipofectamine2000 (ex Invitrogen); HEK293T cells cultured in 5% CO2The culture environment of (1) is 37 ℃, and the culture medium is a DMEM medium containing 10% FBS.
2. Transfection and viral packaging
The first day: the packaging cell line HEK293T was passaged to 10cm dish, approximately 30% confluence;
the next day: transfection was performed at 80% confluence of HEK293T according to the following recipe:
lentiCRISPR v2-SALL1：6μg
pLP1：6μg
pLP2：6μg
pLP/VSVG：3μg
Opti-MEM：500μL。
Lipofectamine 2000：30μL
Opti-MEM：500μL。
after standing for 5min, mix 1 and mix 2 were mixed well to form a transfection mixture, and left to stand for 20 min.
The HEK293T medium was changed to serum-free DMEM medium, the transfection mixture was added, and the medium was changed to 20% FBS DMEM medium after 8 hours at 37 ℃ to continue the culture.
3. Virus collection and preservation
And on the third day: after transfection for 48h, HEK293T medium supernatant containing virus was collected, filtered through 0.45 μm filter tip, split charged, and stored at-80 ℃.
Example four infection of cells of interest and detection of the knockout Effect of the target sequence
1. Material preparation
Culturing porcine hip arterial endothelial cells PIEC (purchased from cell bank of Chinese academy of sciences) of a target cell line; DMEM medium and fetal bovine serum FBS (purchased from Gibco); lentiCRISPR v2-SALL1 pseudotype lentivirus of different target sequences (seq id No. 3 and seq id No. 4); PIEC cells cultured in 5% CO2The culture environment of (1) is 37 ℃, and the culture medium is a DMEM medium containing 10% FBS.
2. Lentiviral infection of target cells
The first day: cells of interest were passaged to 6-well plates at approximately 20% confluency density. One 6 well per virus was required, while one 6 well efficiency control was required.
The next day: 1mL of lentiCRISPR v2-SALL1 pseudotyped lentiviral supernatant and 1mL of DMEM medium were added when the desired cells had a confluency of about 40%. The efficiency control did not require addition of lentivirus.
And on the third day: after 24h of infection, the virus-containing medium was removed, replaced with normal medium, puromycin was added to a final concentration of 2. mu.g/mL, and puromycin was added as a control to the efficiency control sample without virus infection for 48 h.
3. Cell infection efficiency detection and culture
The fifth day: uninfected efficiency control cells should all apoptosis (> 95%) under the action of puromycin. The infection efficiency of the cells is judged according to the apoptosis of infected lentivirus cells, and can generally reach more than 90 percent (the apoptosis rate is less than 10 percent). If necessary, the virus supernatant may be concentrated or diluted in a gradient and then infected to achieve a suitable infection efficiency.
After puromycin screening, uninfected cells were apoptotic. The cells of interest were re-passaged and replaced with normal medium for 48 h.
4. Detection of the Effect of SALL1 Gene knockout
(1) Designing an upstream primer and a downstream primer to amplify the SALL1 gene segment, wherein the sequences of the upstream primer and the downstream primer are shown as follows:
GAGCCCCTCTATGATTAATCGCAATGCA(SEQ ID NO：55)
GTGGGTCCAAGTGTGCGTGAGTG(SEQ ID NO：56)。
the target amplified fragment contains sgRNA target sequence and has the size of 371 bp. The positions of the target sequence from both ends of the fragment are not less than 100 bp.
(2) A part of the cells of interest was collected, and genomic DNA was extracted using a promega genomic DNA kit. Meanwhile, the genome DNA of the wild type target cell is extracted.
(3) The SALL1 gene fragment (including the infected mutant and wild-type samples) containing the target sequence was amplified using genomic DNA as a template.
The amplification reaction (20. mu.L) was as follows:
upstream primer (10 μ M): 1 μ L
Downstream primer (10 μ M): 1 μ L
2×PCR Mix：10μL
Genomic DNA: 100ng
The above reaction system was prepared, placed in a PCR apparatus, and reacted according to the following procedure.
Reaction procedure:
95℃,3min
95℃,30s
58℃,20s
72℃,20s
72℃,3min；
wherein the second through fourth steps are repeated for 35 cycles.
(4) Electrophoresis detection of PCR product and recovery and purification
(5) And (3) respectively heating and denaturing the purified DNA fragments to form hybrid DNA molecules (including mutant samples and wild samples).
The reaction system is as follows:
genomic PCR fragment: 200ng
5 × reaction buffer: 2 μ L
Reaction system totally 9. mu.L
The above reaction system was prepared, placed in a PCR apparatus, and reacted according to the following procedure.
Reaction procedure:
95℃,5min；
80℃,5min；
70℃,5min；
60℃,5min；
50℃,5min；
naturally cooling to room temperature.
(6) Cutting the renatured hybrid DNA (including the mutant and wild-type samples) with the Cruiser enzyme, 1. mu.L of the Cruiser enzyme was added to the denatured, renatured reaction mixture, and incubated at 45 ℃ for 20 min.
(7) And (3) detecting the enzyme digestion product by electrophoresis, and detecting the target sequence mediated SALL1 gene knockout effect.
The digested DNA fragment was analyzed by electrophoresis on a 2% agarose gel at 100V for 25 min. Determining the cutting condition of the target segment and judging the gene knockout effect of the target sequence.
The recognition of the cleavage of the mutated DNA is based on the following principle: infected cells express sgRNA and Cas 9. If targeted cleavage of genomic DNA by sgRNA mediated Cas9 protein, a mutation (wild type to mutant) is introduced near the cleavage site after repair. Because the wild type and the mutant type sequences are not matched at the position, a hybrid molecule formed by the wild type DNA and the mutant type DNA amplified by taking the wild type and the mutant type sequences as templates through renaturation can generate a local loop structure. The latter can be recognized and cleaved by the Cruiser enzyme, resulting in the cleavage of the hybrid DNA molecule into small fragments. The mutant sample contains a part of wild-type DNA component, so that hybrid molecules containing local circular structures can be formed after renaturation.
As a result, as shown in FIG. 5, the wild-type cells which had not undergone viral infection did not produce cleavage, and thus small fragments were not detected; and the sequence 3 and the sequence 4 can effectively target the SALL1 gene to generate cleavage, so that the existence of a small fragment is detected, and the sequence 3 and the sequence 4 can be used as target sequences for CRISPR-Cas9 specific knockout of the pig SALL1 gene.
EXAMPLE five selection and characterization of SALL1 Gene knockout monoclonals
1. Selection of a monoclonal (target sequence based on SEQ ID NO: 3 and SEQ ID NO: 4)
(1) The partially infected target cell population was passaged, and 100 single cells were transferred to 10cm dish culture.
(2) After about 10 days of culture, a significant number of the single clones grew to macroscopic levels.
(3) Individual clones were scraped with a pipette tip and cells were transferred to 24-well plates for culture, one clone per well.
(4) After about one week of culture, some clones grew to a sufficient number and were ready for further characterization.
2. Identification of monoclonal SALL1 knockouts
(1) And collecting the monoclonal and wild cells to be detected, and respectively extracting the genomic DNA.
(2) The SALL1 gene fragments of the monoclonal and wild type cells, respectively, were amplified as described above, with the amplified gene fragment containing the sgRNA target sequence.
(3) Mixing the same amount of monoclonal PCR fragment with wild PCR fragment, heating to denature and renature to form hybrid DNA molecule.
(4) The annealed hybrid DNA was cleaved with Cruiser enzyme and incubated at 45 ℃ for 20 min.
(5) Detecting the enzyme digestion product by electrophoresis, and determining whether effective mutation occurs in the monoclonal according to whether the cutting fragment exists.
The result shows that 20 monoclonals randomly selected from 100 single cells infect target cells based on the lentiCRISPR v2-SALL1 pseudotype lentivirus of the target sequence shown in the sequence 3 and are detected by the enzyme digestion electrophoresis of Cruiser enzyme, wherein 18 monoclonals can detect and cut small fragments, which indicates that gene knockout occurs, and the gene knockout efficiency can reach more than 90 percent, thereby indicating that the target sequence shown in the sequence 3 has high effect of targeted knockout of the SALL1 gene. 20 monoclones randomly selected from 100 single cells infect a target cell based on a lentiCRISPR v2-SALL1 pseudotype lentivirus of a target sequence shown in a sequence 4, and are detected by Cruiser enzyme digestion electrophoresis, wherein 19 monoclones can detect a small cut fragment, which indicates that gene knockout occurs, and the gene knockout efficiency can reach more than 95%, thus indicating that the target sequence shown in the sequence 4 has a very high effect of targeted knockout of the SALL1 gene.
The foregoing is a more detailed description of the present invention that is presented in conjunction with specific embodiments, and the practice of the invention is not to be considered limited to those descriptions. It will be apparent to those skilled in the art that a number of simple derivations or substitutions can be made without departing from the inventive concept.
Claims (8)
1. sgRNA for specifically targeting the SALL1 gene in specific knockout of porcine SALL1 gene using CRISPR-Cas9, characterized in that:
(1) the target sequence of the sgRNA on the SALL1 gene conforms to the sequence arrangement rule of 5 '-N (20) NGG-3', wherein N (20) represents 20 continuous bases, wherein each N represents A or T or C or G, and the target sequence conforming to the rule is positioned on a sense strand or an antisense strand;
(2) the target sequence of the sgRNA on the SALL1 gene is located in the 3 exon coding regions at the N-terminal of the SALL1 gene, or a part of the target sequence is located in the 3 exons at the N-terminal of the SALL1 gene, and the rest of the target sequence spans the boundary with the adjacent intron and is located in the adjacent intron;
(3) the sgRNA is unique in the target sequence on SALL1 gene;
the target sequence is SEQ ID NO: 3 or 4.
Use of sgRNA or its target sequence on SALL1 gene for the preparation of a kit for specific knock-out of porcine SALL1 gene using CRISPR-Cas9, characterized in that the use comprises the steps of:
(1) synthesizing a forward oligonucleotide sequence by adding a sequence for forming a sticky end to the 5' -end of the target sequence of the sgRNA of claim 1; adding appropriate sequences for forming cohesive ends to both ends of a complementary sequence corresponding to a target sequence of the sgRNA according to claim 1, and synthesizing to obtain an inverted oligonucleotide sequence; annealing and renaturing the synthesized forward oligonucleotide sequence and the synthesized reverse oligonucleotide sequence to form double-stranded oligonucleotide with a sticky end;
(2) connecting the double-stranded oligonucleotide into a linearized expression vector carrying a Cas9 gene to obtain an expression vector carrying sgRNA oligonucleotide containing a corresponding target sequence and a Cas9 gene, converting competent bacteria, screening and identifying correct positive clone, shaking the positive clone, and extracting a plasmid;
(3) packaging a pseudolentivirus simultaneously carrying sgRNA of a targeting SALL1 gene and Cas9 by using the expression vector, the packaging plasmid and the packaging cell line which carry the sgRNA oligonucleotide and the Cas9 gene;
(4) infecting a target cell with the pseudotyped lentivirus and further culturing; and then collecting infected target cells, amplifying a gene segment containing the target sequence by using the genome DNA of the infected target cells as a template, and determining the knockout condition of the SALL1 gene through denaturation, renaturation and enzyme digestion.
3. The use of claim 2, wherein the expression vector is SEQ ID NO: 50.
4. Use according to claim 2 or 3, characterized in that it comprises the following steps:
(1) adding a CACCG sequence to the 5' -end of the target sequence of the sgRNA of claim 1, and synthesizing to obtain a forward oligonucleotide sequence; adding an AAAC sequence to the 5 '-end and C to the 3' -end of a complementary sequence corresponding to the target sequence of the sgRNA of claim 1, and synthesizing to obtain an inverse oligonucleotide sequence; annealing and renaturing the synthesized forward oligonucleotide sequence and the synthesized reverse oligonucleotide sequence to form double-stranded oligonucleotide with a sticky end;
(2) and (2) connecting the double-stranded oligonucleotide into a nucleotide sequence shown as SEQ ID NO: 50, obtaining a linear vector by carrying out restriction enzyme digestion on an expression vector lentiCRISPR v2 with a sequence shown in 50 by BsmB I to obtain a recombinant expression vector lentiCRISPR v2-SALL1 carrying sgRNA oligonucleotide, transforming competent bacteria, screening and identifying correct positive clone, shaking the positive clone, and extracting plasmid;
(3) packaging a pseudolentivirus carrying sgRNA of a targeting SALL1 gene and Cas9 simultaneously by using the expression vector lentiCRISPR v2-SALL1, a packaging plasmid and a packaging cell line;
(4) infecting a target cell with the pseudotyped lentivirus and further culturing; and then collecting infected target cells, amplifying a gene segment containing the target sequence by using the genome DNA of the infected target cells as a template, and determining the knockout condition of the SALL1 gene through denaturation, renaturation and enzyme digestion.
5. Use according to claim 4, characterized in that the packaging plasmids are plasmid pLP1, plasmid pLP2 and plasmid pLP/VSVG; the packaging cell line is HEK293T cell.
6. The use according to claim 4, wherein the cell of interest is a porcine PIEC cell;
amplifying a gene segment containing the target sequence by taking the genome DNA as a template, and determining the knockout condition of the SALL1 gene through denaturation, renaturation and enzyme digestion, wherein the steps are as follows:
(a) amplifying a SALL1 gene fragment containing a target sequence of the sgRNA by using the upstream and downstream primers of the SALL1 gene by using the genomic DNA of a target cell infected with the virus as a template, and amplifying the genomic DNA of a wild-type cell not infected with the virus by using the same primer;
(b) purifying the amplified SALL1 gene fragment, and then heating and denaturing and renaturing the SALL1 gene fragment from the target cell infected with virus and the SALL1 gene fragment from the wild cell respectively to form hybrid DNA molecules;
(c) cutting the renatured hybrid DNA molecules by using Cruiser enzyme;
(d) and (3) detecting the enzyme digestion product by electrophoresis, and detecting the target sequence mediated SALL1 gene knockout effect.
7. The recombinant expression vector lentiCRISPR v2-SALL1 used in the method for specifically knocking out pig SALL1 gene by CRISPR-Cas9 is characterized in that the sequence of the skeleton vector of the recombinant expression vector is shown as SEQ ID NO: 50 is shown; the carried target sequence is selected from SEQ ID NO: 3 or 4.
8. Use of the recombinant expression vector lentiCRISPR v2-SALL1 of claim 7 in the preparation of a kit for the specific knockout of porcine SALL1 gene using CRISPR-Cas 9.
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| US9359599B2 (en) | 2013-08-22 | 2016-06-07 | President And Fellows Of Harvard College | Engineered transcription activator-like effector (TALE) domains and uses thereof |
| US9737604B2 (en) | 2013-09-06 | 2017-08-22 | President And Fellows Of Harvard College | Use of cationic lipids to deliver CAS9 |
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| CN101679950A (en) * | 2007-02-22 | 2010-03-24 | 国立大学法人东京大学 | Organ regeneration method utilizing blastocyst complementation |
| CN103820454A (en) * | 2014-03-04 | 2014-05-28 | 黄行许 | Method for human PD1 gene specific knockout through CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat) and sgRNA(single guide RNA)for specially targeting PD1 gene |
| CN104651399A (en) * | 2014-12-31 | 2015-05-27 | 广西大学 | Method for realizing gene knockout in porcine embryonic cells by using CRISPR/Cas system |
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