Generation of single-guide CRISPRi vectors and TeloHAEC derivatives
A. For each guide, order a pair of oligonucleotides (e.g. from IDT... standard non gel-purified guides work well). The oligo sequences will be:
Top: 5'CACCGNNNNNNNNNNNNNNNNNNNN N=guide
Bottom: 5'AAACnnnnnnnnnnnnnnnnnnnnC n=reverse complement of guide
Note: Including a G as the first transcribed base (position 5 on the top strand, and it's reverse complement C as the 3' terminal base on the bottom strand) helps increase guide expression. If the genomic sequence targeted by the guide does not start with a G, add a G to the 5' end of the guide sequence.
Resuspend oligos at 100 µM in water and store frozen at -20C.
1. Digest 5 µg of vector with 50 units of BsmBI restriction enzyme at 55oC for 4 hours (e.g. NEB #R0739S, using manufacturer-supplied buffers). Warning: BsmBI can lose activity soon after it's marked expiration date. If you are not using a new BsmBI stock, check a small sample of this digest on a gel to be sure you see cutting (clean ~7 kb vector and ~1.8kb filler bands before proceeding).
2. SPRI bead purification: Purify by adding 0.7 volumes of SPRIselect beads (SPRI beads, Beckman-Coulter #B23318), mixing and incubating for 5 minutes at room temperature.
3. Place tube in a magnetic stand until beads clear from the solution and adhere to the side.
4. Remove supernatant, and with the tube still on the magnetic stand wash 2x with 1.7 initial volumes of 80% ethanol (removing ethanol by pipette).
5. Briefly spin the tube, put back on the mag stand and remove any remaining ethanol.
6. Let air dry for 5 minutes, then resuspend in 22 µl of water.
7. Let sit for ~ 5 minutes, then put back on the mag stand until the beads clear, and collect 20 µl cut plasmid.
8. Redigest with 25 units BsmBI at 55oC for 2+ hours.
9. Dephosphorylate the 5' ends of the vector by adding 5µl FastAP (ThermoFisher #EF0654) and incubating at 37oC for 20 minutes. Note: this step is omitted when preparing the vector for Gibson cloning of complex guide libraries ("Preparation of lentiviral CRISPRi gRNA library" below).
10. Heat inactivate FastAP at 80oC for 15 minutes.
11. Purify the vector by separation on a 1% agarose gel. If adding loading dye directly to the BsmBI/FastAP reaction results in too great a volume to load, you can perform the SPRI select bead purification from steps 2 though 7 to reduce the volume. Note that gel purification is necessary to remove the ~7kb vector from the ~1.8kb filler sequence.
12. Measure cut, dephosphorylated vector concentration by nanodrop spectrophotometer. Make a working stock at 10ng/µl.
C. Phosphorylate and anneal oligos
In a PCR tube strip, dilute top and bottom guideRNA oligos to 2.5 µM separately in 4 µl water. Add an extra well 4 µl water only to measure self-ligation of backbone.
2. Heat to 85°C for 2 minutes. Quickly transfer to ice.
3. Phosphorylate each oligo (top and bottom, separately) by adding 4 µl of master mix:
10× NEB PNK Buffer 0.8 µl (contains DTT)
NEB T4 PNK (add last) 0.4 µl (NEB T4 polynucleotide kinase, #M0201S)
Note: T4 PNK does not come with ATP, which must be added separately. Alternatively, use NEB T4 DNA Ligase buffer, which includes ATP and in which T4 PNK has 100% activity.
Mix gently but thoroughly, spin down, and incubate at 37°C for 30-60 minutes.
4. Mix Top and Bottom oligos together, denature and slowly anneal them in a PCR machine:
2 min 98°C, 2 min 85°C, 5 min 75°C, 5 min 65°C, 10 min 22°C.
D. Ligation, Transformation and confirmation of guide inserts
Make the following master mix (in this order) and combine 5 µl mix with 5 µl annealed oligos from above.
10× NEB T4 DNA Ligase Buffer 1µl
BsmBI-digested vector (10ng/µl) 1 µl
NEB T4 DNA Ligase (add last) 0.5µl. (New England Biolabs Inc #M0202S)
(annealed oligo mix) (5µl)
2. Incubate at room temperature for 30 minutes.
3. Thaw competent NEB 5-alpha cells (New England Biolabs #C2987I, or, alternatively, NEB stable) on ice.
4. Chill ligation reaction on ice and add 1 µl ligation reaction to 5 µl cells. Mix
gently.
5. Incubate on ice for 20 min.
6. Heat shock 42°C for 40 seconds, then return to ice for 2 minutes.
7. Add 50 µl SOC media (provided with competent cells) and incubate at 30°C for 1 hour with shaking.
8. Streak out onto carbenicillin (a more stable analog of ampicillin, Sigma, C3416_5g, or equivalent) plates (50 µg/ml) and incubate overnight at 30°C.
9. Pick colonies, and grow in 3 ml LB plus carbenicillin (50µg/ml) at 30°C overnight.
10. Miniprep the DNA and send for Sanger sequencing using primers flanking the BsmBI insertion site.
Guide reference: Some guides from our studies that we have validated as effective for knock down of target gene expression in CRISPRi TeloHAEC (TargetGene_CloneIndex: ForwardSequence) are: CCM2_C2: GGCAAGAAGGTGAGCGTGCG, CCM2_F6: GAGCCGCTACATGCTCGACCC, CDH5_B8: GCCAGCTGGAAAACCTGAAG, CDH5_D5: GTTGGACTGCCTGTCCGTCCA, ITGB1BP1_C7: GAAGGCCGCGGCACTCCCACG, ITGB1BP1_G8: GAAGTCCGCAACCCGGGGAT, KLF2_C9: GGACCCGGGGAGAAAGGACG, KLF2_G10: GCCGCGGTATATAAGCCGGC, MAP2K5_B5: GTCTGCCCCACCCGGAGACAC, MAP3K3_A4: GTTCCTGAGGTGGAGAACGG, MAP3K3_C3: GCCAATAACAAGAAGGAAGT, MEF2A_C10: GCGGCGCGAAGCGCTGGTGG, MEF2A_H10: GACTGAATTATCCTCTCGGT, NFAT5_D4: GGCCTCGCTTCCTGCCGGCG, NFAT5_D7: GGTCCCCGTCCCGCCGGGGG, PDCD10_D11: GACCGAGCAGAAGAGGTCTA, PDCD10_G1: GCCGCTTTACGCCACTCGCGT, TLNRD1_B3: GTGGCTGCGCCGCCGCCCGCA, TLNRD1_D12: GCCTCCGGCAGCCCCTGCGGG. If any of these genes is expressed well in your model cell line, these should work as effective positive controls to test your CRISPRi cell line.
For negative controls, we used nontargeting guides: Negative_control_B6: GCAACGGTGTACCGCGGATC, Negative_control_D2: GTGGTTCACAACCGGACCCA, Negative_control_D8: GGTGGTTCGGTTTGCGTGGCC, Negative_control_F4: GCTGGGCGGACGTTGGGATA,
One guide, MAP2K5_A11: GCCGAGGCCGCGCGGACTGG, was not effective.