2.1 DLX5a knock down
Selection and confirmation of CasRx target sites
The mRNA sequence for the of zebrafish zDLX5a gene was identified and downloaded from the NCBI platform (National Center for Biotechnology Information (nih.gov), and the transcript sequence of the target gene was identified on the Ensembl platform (Ensembl genome browser 104). The sequence was analyzed by Snapgene software and compared with the mRNA sequence of the target gene; we then designed a target sequence within the common region. Once the target sequence was confirmed, its specificity was verified on the Ensembl platform (Ensembl genome browser 104).
Preparation of gRNA
PCR amplification was used to bridge the double-stranded DNA template with suitable primer pairs, and then T7 RNA polymerase (NEB; cat#M0251S) was used to synthesize gRNA. Next the gRNA was digested with DNase I (NEB; cat#M0303S) for 15 min to remove the DNA template, and then purified with a Post-reaction Clean-up Kit (Sigma).
The gRNA primer pairs were as follows:
zDLX5a-CasRx-F: GAAATTAATACGACTCACTATAGGcactagtgcgaatttg cactagtctaaaac
zDLX5a-KD-gRNA-R1: ACATCTACATCACAGATAGCCAgttttagactagtgc aaa
zDLX5a-KD-gRNA-R2: TACAAGGAGACGGTCAGGATGTgttttagactagtg caaa
gRNA template synthesis
PCR reactions were prepared as described in Table1.
Table 1. Constituents of PCR reactions
Reagents
|
Volume/μL
|
2 × PCR mix
|
50
|
Forward Primer(10 μM)
|
16
|
Reverse Primer(10 μM)
|
16
|
H2O
|
18
|
Total
|
100
|
First, we prepared 100-200 μL reactions and ensured that the concentration of DNA template obtained by recovery and purification exceeded 100 ng/μL. The template was divided equally into two tubes for PCR. The PCR program was as follows: preheating at 98 ℃ for 30 s, denaturation at 98 ℃ for 10 s, annealing at 55 ℃ for 30 s, extension at 72 ℃ for 15 s, and continuous extension at 72 ℃ for 10 min,12 ℃.
Purification of the gRNA template. First. 0.6g of Agar powder (OXOID, LP0028A) was mixed with 60 mL TAE buffer in a conical bottle and heated in microwave oven until clarified. Once the solution had cooled, added 6 μL of nucleic acid stain. The molten gel was used to create a gel for electrophoresis.
Following electrophoresis, the separated DNA bands were cut and placed in an RNase-free centrifuge tube. The gel was weighed and three times its volume of PE solution was added. Then, the gel was dissolved by placing the tube in a water bath at 56℃ until the gel was completely dissolved and preheat with RNase-free H2O. The final solution (800-900 μL) was added to an adsorption column and left for 2 min. Then, the solution was centrifuged at 12000 rpm for 1min. The liquid was aspirated from the collecting tube, left for 2min, and then centrifuged at 12000 rpm for 1min. Then, we discarded the liquid in the collection tube and added 600 uL of rinse solution (PW). The tube was left for 2 min and then centrifuged at 12000 rpm for 1 min. The waste liquid was then discarded, and the centrifugal column was placed back into the collection tube and spun at 12000 rpm for 3min. Next, the column was transferred to an RNase-free centrifuge tube and air-dried on a clean table for 5 min. Preheated RNase-free H2O was then dripped into the middle of the adsorption film; we measured the brightness of the electrophoretic band and the volume of recovery (30-50 μL). After 5 min incubation at room temperature, the sample was centrifuged at 12000 rpm for 3 min.
Transcription and purification of gRNA in vitro. The in vitro transcription system was prepared as follows:
Table 2. The in vitro transcription system
Reagents
|
Volume/μL
|
10 × T7 Reaction Buffer
|
2
|
ATP
|
2
|
CTP
|
2
|
GTP
|
2
|
UTP
|
2
|
RNA inhibitor
|
0.5
|
Template DNA (Approx. 500 ng)
|
2
|
T7 Enzyme Mix
|
2
|
H2O(RNase-free)
|
5.5
|
The reaction solution was incubated at 37 ℃ for 4 h.
The purification of gRNA
The prepared reaction solution was added to the same volume of LiCl solution and incubated overnight at -20 ℃. On the second day, the solution was centrifuged at 13000 rpm for 10 min at 4 ℃. Following centrifugation, the supernatant was discarded and washed twice with 75% RNase-free ethanol. The solution was then centrifuged at 13000 rpm for 5 min and the supernatant was discarded. After the liquid was thoroughly absorbed and air-dried, we added 30 μL of RNase-free water. Then, we measured the concentration and stored the gRNA at-80 ℃.
2.2 The preparation of CasRx mRNA
The pXR001 plasmid was purchased from Addgene and used as the template for CasRx. Primers were designed to amplify CasRx DNA. Capped CasRx mRNA was synthesized by a mMESSAGE mMACHINE SP6 Transcription Kit (Invitrogen) and then purified in accordance with the purification procedure described earlier (Ambion; cat#AM1344/T7 RNA polymerase; cat#AM1348/T3 RNA polymerase).
CasRx DNA template preparation
CasRx DNA reaction system and reaction conditions were as follows:
Table 3. The CasRx DNA reaction system and reaction conditions
Reagents
|
Volume/μL
|
Temperature
|
Time
|
|
Primer STAR
|
25
|
98℃
|
3 min
|
|
Primer F(10 μmol)
|
1
|
98℃
|
15 s
|
35 cycles
|
Primer R(10 μmol)
|
1
|
55℃
|
45 s
|
Template
|
1
|
72℃
|
2 min
|
ddH2O
|
22
|
72℃
|
10 min
|
|
|
50
|
12℃
|
10 min
|
Stored
|
Purification of the CasRx DNA template
The CasRx DNA template was prepared in the same manner as gRNA.
CasRx mRNA transcription in vitro
The reaction system was as shown in Table 4:
Table 4. The CasRx mRNA transcription system
Reagents
|
Volume/μL
|
10 × Reaction buffer
|
2
|
2 × NTP/CTP
|
10
|
SP6 Enzyme
|
2
|
Template(> 500 ng)
|
5.5
|
RIn
|
0.5
|
The reactions were carried out at 37 ℃ for 4 h, (hot cap 70 ℃) 1 μL DNAase, 37 ℃, digested 30 min.
The reaction system with poly A tail is shown in Table 5.
Table 5. The reaction system with poly A tail
Reagents
|
Volume/μL
|
IVT reaction solution
|
20.5
|
H2O
|
36
|
5 × EAP Buffer
|
20
|
ATP
|
10
|
Mncl2
|
10
|
E-PAP enzyme
|
3.8
|
Total
|
100
|
The reaction was carried out at 37 ℃ for 1 h (hot cover 70 ℃).
Purified CasRx mRNA
CasRx mRNA was purified in the same manner as gRNA.
2.3 Microinjection of zebrafish embryos
Primer design
The sequences of the primers are shown below.
F: ATCCGTCTCAGGAATCTCCAACC
R: TAATACGACTCACTATAGGGATCCGAGTGCCAACGAGTGTAA
Preparation of the linear template DNA
The PCR reactions were prepared as shown in Table 6.
Table 6. PCR reactions
Reagents
|
Volume
|
2×Taq Master Mix
|
50.0 μL
|
cDNA
|
4.0 μL
|
Forward Primer(10 μM)
|
6.0 μL
|
Reverse Primer(10 μM)
|
6.0 μL
|
Add H2O
|
To 100 μL
|
The PCR reaction procedure as follows: 94 ℃ 5 min; 94 ℃ 10 s, 60 ℃ 15 s, 72 ℃ 42, 32 cycles; 72 ℃ 5 min. Amplicons were analyzed by 1% agarose electrophoresis detection.
Preparation and purification of the probe
The probe was prepared as described in Table 7.
Table 7. Preparation of the probe
Reagents
|
Volume
|
Linear Template DNA
|
To 1μg
|
10x Transcription buffer
|
1.0 μL
|
DTT 50 mM
|
1.0 μL
|
DIG-RNA labeling mix (UTP)
|
1.0 μL
|
RNAsein (40U/μL)
|
0.5 μL
|
T3 or T7 RNA polymerase (20U/μL)
|
0.5 μL
|
RNase free Water
|
To 10 μL
|
The reagent was mixed well and incubated in a 37 °C water bath for 3-4 hours. Then, we added 2 μL of RNAse-free DNAse I and 18 μL of RNAse-free H2O to the 10 μL reaction system; this was then incubated for 30 min at 37 °C. Next, 1 μL of 0.5M EDTA (RNAse-free) was added to terminate the reaction. A Sigma Spin Post Reaction Purification Column was placed into the collection tube and centrifuged at 2800 rpm at 4 ℃ for 15 s. The purification column was removed from the tail and lid, and then centrifuged at 2800 rpm and 4 ℃ for 2 min. The purified column was then transferred into a new RNAse-free microcentrifuge tube and mixed with RNA reaction solution before being centrifuged at 2800 rpm (4 ℃) for 4 min. The purity of the probe was evaluated by electrophoresis and the probe was stored at -80 ℃ for use.
In situ hybridization
Embryos were microinjected 0-15 min after fertilization. The egg membrane was removed after 24 hours. Zebrafish embryos that had developed to the appropriate stage were selected and fixed in 4%PFA-PBS. Pigmentation was removed by incubation in 0.5% KOH + 3% H2O2; then, the embryos were fixed overnight in methanol at-20 ℃. The preserved embryos were removed and passed through 75% methanol / 25%PBS, 50% methanol / 50%PBS, 25% methanol / 75%PBS and PBT (5 min each time). Then, the embryos were washed for 5 min with PBT (PBT; 0.1%Tween-20 in PBS). After digestion with 1 mL of 10 μg/mL protease K solution (embryos prior to the Bud stage did not need to be digested; 24 hpf embryos were digested for 10 min; 36 hpf embryos were digested for 20 min; 48 hpf embryos were digested for 30 min). Then, we removed protease K and added 4% PFA-PBS for 20 min to stop enzyme digestion. Then, the embryos were washed five times with PBT (5 min per wash). Then, we added an appropriate amount of pre-hybridization solution followed by incubation in a water bath at 70 ℃ for 3-4 hours. The probe was diluted in hybrid solution to 1 μg/mL and hybridized overnight in a water bath at 70℃. The probe was then recycled at -20℃. The embryos was incubated at 75% HM/25% 2 × SSC, 70 ℃ 10 min; 50% HM/50% 2 × SSC,70 ℃ 10 min; 25% HM/75% 2 × SSC, 70 ℃ 10 min; 2 × SSC, 70 ℃ 10 min; 0.2 × SSC, 70 ℃ 30 min; 0.2 × SSC, 70 ℃ 30 min; 75% 0.2 × SSC/25% PBT, room temperature 10 min; 50% 0.2 × SSC/50% PBT, room temperature 10 min; 25% 0.2 × SSC/75% PBT, incubated at room temperature for 10 min; PBT, incubated at room temperature for 10 min. Next, we added an appropriate amount of sealing solution to the embryos; this was followed by incubation at low speed on a shaker for 3-4 h at room temperature. An alkaline phosphatase-coupled digoxin antibody was then diluted with fresh sealing solution (the dilution ratio was 1: 5 000) and placed on a horizontal shaker overnight at 4 ℃ with gentle shaking. The antibody reaction solution was then discarded, and the embryos were rinsed six times with PBT at room temperature (15 min per wash). Next, we removed the PBT as much as possible and rinse the embryos three times with alkaline tris buffer at room temperature (5 min per wash). We removed the alkaline tris buffer, added freshly configured chromogenic solution (labeling solution) and allowed color to develop in the absence of light at room temperature or overnight at 4℃. We observed the chromogenic effects at regular intervals and terminated the chromogenic reaction when the positive signals appeared blue-purple. The chromogenic solution was then removed and an appropriate amount of terminating solution was added. The embryos were then rinsed three times at room temperature; followed by 10 min, 30 min, and 1 h. The embryos were transferred into 100% glycerol and balanced it overnight at low speed on a shaker at 4 ℃. The next day, we used an Olympus microscope to acquire photographs. The experiment was divided into two groups as follows: the CasRx control group (CasRx) and the SgRNA knock-down group (zDLX5a-sgRNA1+zDLX5a-sgRNA2+CasRx).
2.4 Detection of target gene expression by fluorescence quantitative PCR
Extraction of total RNA: Total RNA was extracted by placing the sample into a 2 mL microcentrifuge tube (RNase-free) and mixed with 1 mL of RNAiso Plus. Samples were then homogenized and placed at room temperature for 5 min. The supernatant was then transferred to a fresh 1.5 mL microcentrifuge and RNA was extracted using a conventional chloroform/ isopropanol procedure. Extracted RNA was resuspended in 30 μL RNase-free ultra-pure water and stored at-70 ℃.
The determination of RNA extraction quality: The nucleic acid concentration and A260/A280 value of RNA extracted from each sample were accurately measured and recorded by a nucleic acid concentration meter. RNA integrity was determined by 2% agarose gel electrophoresis in 1 × TBE buffer; 2 μL of total RNA was mixed with 0.5 μL of 6 × buffer and loaded onto the gel. The gel was run for 15 min at a voltage of 110V and 30-50 mA.
Reverse transcription synthesis of cDNA: The reaction system was prepared in accordance with the manufacturer’s instructions (NovoScript ®1st Strand cDNA Synthesis SuperMix).
Primer sequences: ef1 α was selected as the internal reference gene. Fluorescent PCR primers were designed for each gene using primer5 software. Following BLAST comparisons, the primers were synthesized by Fuzhou Shangya Biology Co., Ltd.
The primers are as follows:
Table 8. Primer sequences
Gene name
|
Primer sequence (5’-3’)
|
Amplified fragment length length
|
zDLX5a
|
F:TATTGTTCACCGAACTCGGGC
|
198 bp
|
|
R:TGTTTCTTTTTCTTGCGGGC
|
ef1α
|
F:CTTCTCAGGCTGACTGTGC
|
358 bp
|
|
R:CCGCTAGCATTACCCTCC
|
DKK1
|
F:TAGCACCTTGGATGGGTATTC
|
108 bp
|
|
R:CCTGAGGCACAGTCTGATGAC
|
BOZ
|
F:GGATGTACTGCTGCTGCGTT
|
174 bp
|
|
R:GCTGCTCCGTCTGGTTGTCG
|
OTX2
|
F:TGTGCTGGAGGCTTTATTCG
|
128 bp
|
|
R:GACACTTTGCCCTTCGGTTT
|
Wnt8a
|
F:TGCCACCAGAGAGACCGCCT
|
144 bp
|
|
R:ACCCAACCACGACCACCCAT
|
tbx6
|
F:AACACTGGCAGAACCGCACC
|
148 bp
|
|
R:CCCCACATCAGCACATCACG
|
Notch1b
|
F:CAGCATCCACAACTACAGGT
|
132 bp
|
|
R:CAGAGGAAGTCCGAATCAAA
|
deltaC
|
F:GAAACCTGGAACGCAGAAAC
|
164 bp
|
|
R:TCGCACACGACACGATAAGA
|
Fluorescence quantitative PCR. First, the specificity of the primers was verified by routine PCR. Then, a fluorescent quantitative PCR test was carried out using the ChamQ SYBR qPCR Master Mix (Q331-02) kit. The results of fluorescence PCR were determined by the 2-△△CT method. All data were analyzed by GraphPad Prism version and differences between groups were compared by one-way analysis of variance (ANOVA). Differences were statistically significant if P < 0.05.
2.5 Brain volume measurement
Microphotography
Zebrafish were allowed to develop to 48 hpf, 72 hpf and 96 hpf after injection and then placed in methylcellulose solution in the prone position. Images of each whole fish were then acquired on an inverted microscope (Nikon, SMZ745T) at two different magnifications (3X and 7X).
Statistical methods for brain volume. Photographs were imported into Image J software and adjusted to 8 bits. Then, we used the software to circle the brain; the software automatically calculated the brain volume.
2.6 Behavior trajectory analysis
Trajectory was analyzed with Noldus EthoVision XT software. The track capture time was 10min, and the analysis index included the trajectory moving distance and the trajectory moving average speed.
2.7 Data processing
Data were statistically analyzed by SPSS version 19.0 software package and expressed as mean ± standard deviation (SD). Differences between groups were compared by one-wat analysis of variance (ANOVA); α = 0.05 and P<0.05 was statistically significant. GraphPad Prism 8 was used to plot figures.