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The present protocol describes a single-cell method for iterative epigenomic analyses using a reusable single cell. The reusable single cell allows analyses of multiple epigenetic marks in the same single cell and statistical validation of the results.
Current single-cell epigenome analyses are designed for single use. The cell is discarded after a single use, preventing analysis of multiple epigenetic marks in a single cell and requiring data from other cells to distinguish signal from experimental background noise in a single cell. This paper describes a method to reuse the same single cell for iterative epigenomic analyses.
In this experimental method, cellular proteins are first anchored to a polyacrylamide polymer instead of crosslinking them to protein and DNA, alleviating structural bias. This critical step allows repeated experiments with the same single cell. Next, a random primer with a scaffold sequence for proximity ligation is annealed to the genomic DNA, and the genomic sequence is added to the primer by extension using a DNA polymerase. Subsequently, an antibody against an epigenetic marker and control IgG, each labeled with different DNA probes, are bound to the respective targets in the same single cell.
Proximity ligation is induced between the random primer and the antibody by adding a connector DNA with complementary sequences to the scaffold sequence of the random primer and the antibody-DNA probe. This approach integrates antibody information and nearby genome sequences in a single DNA product of proximity ligation. By enabling repeated experiments with the same single cell, this method allows an increase in data density from a rare cell and statistical analysis using only IgG and antibody data from the same cell. The reusable single cells prepared by this method can be stored for at least a few months and reused later to broaden epigenetic characterization and increase data density. This method provides flexibility to researchers and their projects.
Single-cell technology is entering the era of single-cell multiomics, which integrates individual single-cell omics technologies1. Recently, single-cell transcriptomics has been combined with methods for detecting chromatin accessibility (scNMT-seq2 and SHARE-seq3) or histone modifications (Paired-seq4 and Paired-Tag5). More recently, single-cell transcriptomics and proteomics were integrated with chromatin accessibility (DOGMA-seq6). These methods use transposase-based tagging for detecting chromatin accessibility or histone modifications.
Transposase-based approaches cleave genomic DNA and add a DNA barcode at the end of the genomic DNA fragment. Each cleaved genomic fragment can only accept up to two DNA barcodes (= one epigenetic mark per cleavage site), and the genomic DNA at the cleavage site is lost. Therefore, cleavage-based approaches have a trade-off between the number of epigenetic marks tested and the signal density. This hampers the analysis of multiple epigenetic marks in the same single cell. A single-cell epigenomic method that does not cleave the genomic DNA was developed to overcome this issue7,8.
In addition to the cleavage-derived issue mentioned above, transposase-based approaches have other limitations. In single-cell epigenome analysis, it is critical to know the location of histones and DNA-associated proteins on the genome. In current approaches, this is accomplished by using unfixed single cells and retention of protein-DNA and protein-protein interactions. However, this generates strong bias to accessible chromatin regions, even in the analysis of histone modifications 9. The location of histones and genome-associated proteins on the genome can be preserved without crosslinking protein-DNA and protein-protein, using a polyacrylamide scaffold7,8. This approach reduces the structural bias observed in current approaches that depend upon protein-DNA and protein-protein interactions.
Transposase-based approaches can acquire signals only once from a single cell. Therefore, it is difficult to delineate the complete epigenome of a single cell due to the drop-off of the signals. Reusable single cells have been developed to overcome current limitations by allowing iterative epigenomic analysis in the same single cell.
NOTE: A schematic representation of the method is shown in Figure 1.
Figure 1: Schematic representation of the protocol workflow. Steps 7.2-13 are explained through schematic representations. Each row indicates a step in the protocol. A cellular protein colored in green is a human nucleosome generated based on a crystal structure (PDB: 6M4G). Please click here to view a larger version of this figure.
1. Equilibration of desalting columns
NOTE: Desalting spin columns are equilibrated as described in the following steps. The equilibrated desalting columns are used in steps 2.1, 3.4, and 4.6.
2. Buffer exchange of antibodies
NOTE: Remove glycerol, arginine, and sodium azide from anti-H3K27ac10, anti-H3K27me310, anti-Med111, and anti-Pol II10 (see buffer composition shown in Table 1). All following procedures are performed under a clean hood to avoid DNase contamination. Time: 1 h
3. Antibody activation
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 2.5 h
4. Activation of DNA probe
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 2.5 h
5. Conjugation of S-HyNic-modified antibody and S-4FB-modified Antibody Probe
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 2 h
6. Preparation of core magnetic beads
NOTE: In this method, a single cell is embedded into a bilayered acrylamide bead (see Figure 2). The core is a magnetic polyacrylamide bead. The outer layer is polyacrylamide alone. The core magnetic beads are generated in this section. This section is not essential for the experiment. Time: 3 h
Figure 2: Structure of a bilayered polyacrylamide bead for visibility and easy handling in REpi-seq experiments. (A) Magnetic nanoparticles from step 6.6 after centrifugation. The magnetic nanoparticles are modified with monomeric acrylamide and integrated into the polyacrylamide magnetic bead shown in B.(B) Schematic representation of a reusable single cell with a polyacrylamide magnetic bead. Please click here to view a larger version of this figure.
7. Modifying the amino group of cellular proteins with monomer acrylamide
NOTE: REpi-seq was designed to analyze the epigenome of mouse and human cells at the single-cell level. Each step must be optimized when using this method on cells of species other than mouse or human.
8. Preparation of reusable single cells
Figure 3: Automatic single-cell picking and transfer into a 96-well PCR plate in step 8.2. (A) Overview of a single cell-picking system. A single cell-picking robot is in a laminar flow clean hood to avoid contamination. (B) A 24-well plate with 4 nL nanowells inside the well. (C) Cell distribution in a well from the 24-well plate. Green dots are cells identified as a single cell in each 4 nL nanowell. Magenta dots are cells identified as doublets or multiplets of cells. (D) Brightfield image of the well in the 24-well plate. A green square is a 4 nL nanowell containing a single cell. A magenta square is a 4 nL nanowell containing multiple cells. (E) Magnified field of some 4 nL nanowells. Bright dots are single cells in 4 nL nanowells. The single cell-picking system identifies nanowells containing a single cell by acquiring brightfield and fluorescence images of cells with DAPI staining. Identified single cells are transferred from the 4 nL nanowell to a well of a 96-well PCR plate. Scale bars = 2 mm (C, D), 100 µm (E). Abbreviation = DAPI = 4',6-diamidino-2-phenylindole. Please click here to view a larger version of this figure.
Figure 4: Generating reusable single cells using a liquid-handling robot. (A) A deck of the liquid-handling robot. The deck has 11 slots for pipette tip racks (P300 tip: Slots 1-3, P20 tip: Slots 5-6), 2 mL deep-well 96-well plate (Slot 4), two 96-well PCR plates containing a single cell per well (Slots 7 and 10), and two flat-bottom 96-well plates for liquid waste (Slots 8 and 11). (B) The deck after placing the labware. (C) Schematic representation of robotic pipetting in step 8.8.1. The program removes the supernatant without aspirating a single cell from the bottom of the 96-well PCR plate. (D) Reusable single cells generated using the Supplemental Code 1. Please click here to view a larger version of this figure.
9. Random primer annealing and extension
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Asterisks (*) at the following steps indicate that a magnetic separator can be used to control the position of the polyacrylamide beads containing a reusable single cell in the tube. However, the use of the magnetic separator is not essential. By moving down the pipette tip slowly along the wall of the tube, the beads are pushed up for washing or buffer exchange. Time: 9 h
10. Antibody binding
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 1.5 h
11. Proximity ligation of antibody probe and proximally extended random primer
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Asterisks (*) in the following steps indicate where a magnetic separator can be used to control the position of polyacrylamide beads containing a reusable single cell in the tube. However, the use of the magnetic separator is not essential. By moving down the pipette tip slowly along the wall of the tube, the beads can be pushed up for washing or buffer exchange. Time: 6 h
12. Full extension of the 1st random primer
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 4.5 h
13. Multiple displacement amplification
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 2.5 h (steps 13.1-13.2) + 15 min (steps 13.3-13.4) + 1 day (steps 13.5-13.10)
14. Phenol-chloroform purification and polyethylene glycol precipitation
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 1.5 h
15. In vitro transcription
NOTE: The following procedure is performed under a clean hood to avoid DNase and RNase contamination. Time: 5 h
16. RNA purification
NOTE: The following procedure is performed under a clean hood to avoid DNase and RNase contamination. Time: 2 h
17. Reverse transcription
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 1 h
18. Second strand synthesis
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 2.5 h
19. Restriction enzyme digestion and size selection
NOTE: The following procedure is performed under a clean hood to avoid DNase contamination. Time: 3 h (steps 19.1-19.7)
K562 single cells were generated using the protocol described in step 8 (see Figure 5). Single cells were embedded in the outer layer of the polyacrylamide bead. Cell DNA was stained and visualized using an intercalator dye for DNA staining.
Figure 5: Generated reusable single cells. Cells are sta...
This article describes the step-by-step protocol for the recently reported single-cell multiepigenomic analysis using reusable single cells7. In the subsequent paragraphs, we discuss critical points, emphasizing potential limitations in the protocol.
One of the critical points throughout the protocol (from steps 7.2-13) is avoiding DNase contamination. A single cell only has two copies of genomic DNA. Therefore, damaging genomic DNA critically reduces the signal number...
Drs. Ohnuki and Tosato are co-inventors on a patent entitled "Methods for preparing a reusable single cell and methods for analyzing the epigenome, transcriptome and genome of a single cell" (EP3619307 and US20200102604). The patent application was filed in part based on preliminary results related to the technology described in the current manuscript. The invention or inventions described and claimed in this patent application were made while the inventors were full-time employees of the U.S. Government. Therefore, under 45 Code of Federal Regulations Part 7, all rights, title, and interest to this patent application have been or should by law be assigned to the U.S. Government. The U.S. Government conveys a portion of the royalties it receives to its employee inventors under 15 U.S. Code § 3710c.
We thank Drs. David Sanchez-Martin and Christopher B. Buck for comments during the conceptualization stage of the project. We also thank the Genomics Core, Center for Cancer Research, National Cancer Institute, National Institutes of Health for help in preliminary experiments, and the Collaborative Bioinformatics Resource, CCR, NCI, NIH for advice in computational analysis. We thank Ms. Anna Word for helping with the optimization of DNA polymerases used in the method. This work utilized the computational resources of the NIHHPC Biowulf cluster (http://hpc.nih.gov). This project is supported by the Intramural Program of the Center for Cancer Research, National Cancer Institute, National Institutes of Health, the NCI Director's Innovation Award (#397172), and Federal funds from the National Cancer Institute under Contract No. HHSN261200800001E. We thank Drs. Tom Misteli, Carol Thiele, Douglas R. Lowy, and all members of Laboratory of Cellular Oncology for productive comments.
Name | Company | Catalog Number | Comments |
10x CutSmart buffer | New England BioLabs | B6004 | 10x Digestion buffer |
200 proof ethanol | Warner-Graham Company | 200 proof | Ethanol |
5-Hydroxymethylcytosine (5-hmC) Monoclonal Antibody [HMC/4D9] | Epigentek | A-1018-100 | Anti-5hmC |
Acridine Orange/Propidium Iodide Stain | Logos Biosystems | F23001 | Cell counter |
Acrylamide solution, 40% in H2O, for molecular biology | MilliporeSigma | 01697-500ML | 40% acrylamide solution |
All-in-One Fluorescence Microscope BZ-X710 | Keyence | BZ-X710 | Scanning microscope |
Amicon Ultra-0.5 Centrifugal Filter Unit | MilliporeSigma | UFC510024 | Ultrafiltration cassette |
Ammonium persulfate for molecular biology | MilliporeSigma | A3678-100G | Ammonium persulfate powder |
Anhydrous DMF | Vector laboratories | S-4001-005 | Anhydrous N,N-dimethylformamide (DMF) |
Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody [4H8] | Abcam | ab5408 | Anti-Pol II |
Anti-TRAP220/MED1 (phospho T1457) antibody | Abcam | ab60950 | Anti-Med1 |
BciVI | New England BioLabs | R0596L | BciVI |
Bovine Serum Albumin solution, 20 mg/mL in H2O, low bioburden, protease-free, for molecular biology | MilliporeSigma | B8667-5ML | 20% BSA (Table 7) |
Bst DNA Polymerase, Large Fragment | New England BioLabs | M0275L | Bst DNA polymerase |
BT10 Series 10 µl Barrier Tip | NEPTUNE | BT10 | P10 low-retention tip |
CellCelector | Automated Lab Solutions | N/A | Automated single cell picking robot |
CellCelector 4 nl nanowell plates for single cell cloning, Plate S200-100 100K, 24 well,ULA | Automated Lab Solutions | CC0079 | 4 nL nanowell plate |
Chloroform | MilliporeSigma | Chloroform | |
Corning Costar 96-Well, Cell Culture-Treated, Flat-Bottom Microplate | Corning | 3596 | Flat-bottom 96-well plates |
Deep Vent (exo-) DNA Polymerase | New England BioLabs | M0259L | Exo- DNA polymerase |
DNA LoBind Tubes, 0.5 mL | Eppendorf | 30108035 | 0.5 mL DNA low-binding tube |
DNA Oligo, 1st random primer | Integrated DNA Technologies | N/A, see Table 3 | 1st random primer |
DNA Oligo, 2nd random primer Cell#01 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#02 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#03 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#04 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#05 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#06 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#07 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#08 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#09 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#10 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#11 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd random primer Cell#12 | Integrated DNA Technologies | N/A, see Table 3 | 2nd random primer |
DNA Oligo, 2nd synthesis primer | Integrated DNA Technologies | N/A, see Table 3 | 2nd synthesis primer |
DNA Oligo, Ligation Adaptor | Integrated DNA Technologies | N/A, see Table 3 | Ligation Adaptor |
DNA Oligo, Reverse Transcription primer | Integrated DNA Technologies | N/A, see Table 3 | Reverse Transcription primer |
DNase I (RNase-free) | New England BioLabs | M0303L | DNase I (RNase-free, 4 U). |
DNase I Reaction Buffer | New England BioLabs | B0303S | 10x DNase I buffer (NEB) |
dNTP Mix (10 mM each) | Thermo Fisher | R0192 | 10 mM dNTPs |
Fetal Bovine Serum, USA origin, Heat-inactivated | MilliporeSigma | F4135-500ML | Fetal bovine serum |
HiScribe T7 High Yield RNA Synthesis Kit | New England BioLabs | E2040S | In-vitro-transcription master mix |
Histone H3K27ac antibody | Active motif | 39133 | Anti-H3K27ac |
Histone H3K27me3 antibody | Active motif | 39155 | Anti-H3K27me3 |
IgG from rabbit serum | Millipore Sigma | I5006-10MG | Control IgG |
Iron oxide(II,III) magnetic nanopowder, 30 nm avg. part. size (TEM), NHS ester functionalized | MilliporeSigma | 747467-1G | NHS ester functionalized 30 nm iron oxide powder |
K-562 | American Type Culture Collection (ATCC) | CCL-243 | cells |
Linear Acrylamide (5 mg/mL) | Thermo Fisher | AM9520 | Linear Acrylamide |
LUNA-FL Dual Fluorescence Cell Counter | Logos Biosystems | L20001 | Cell counter |
LUNA Cell Counting Slides, 50 Slides | Logos Biosystems | L12001 | Cell counter |
Mineral oil, BioReagent, for molecular biology, light oil | MilliporeSigma | M5904-500ML | Mineral oil |
N,N,N′,N′-Tetramethylethylenediamine for molecular biology | MilliporeSigma | T7024-100ML | N,N,N′,N′-Tetramethylethylenediamine |
NaCl (5 M), RNase-free | Thermo Fisher | AM9760G | 5M NaCl |
NanoDrop Lite | Thermo Fisher | 2516 | Microvolume spectrophotometer |
NEST 2 mL 96-Well Deep Well Plate, V Bottom | Opentrons | N/A | 2 mL deep well 96-well plate |
Non-skirted 96-well PCR plate | Genesee Scientific | 27-405 | 96-well PCR plate |
NuSive GTG Agarose | Lonza | 50081 | Agarose |
OmniPur Acrylamide: Bis-acrylamide 19:1, 40% Solution | MilliporeSigma | 1300-500ML | 40%Acrylamide/Bis-acrylamide |
OT-2 lab robot | Opentrons | OT2 | Automated liquid handling robot |
Paraformaldehyde, EM Grade, Purified, 20% Aqueous Solution | Electron Microscopy Sciences | 15713 | 20% Pararmaldehyde |
PBS (10x), pH 7.4 | Thermo Fisher | 70011044 | 10x PBS |
PIPETMAN Classic P1000 | GILSON | F123602 | A P1000 pipette |
Protein LoBind Tubes, 1.5 mL | Eppendorf | 925000090 | 1.5 mL Protein low-binding tube |
QIAgen Gel Extraction kit | Qiagen | 28706 | A P1000 pipette |
Quant-iT PicoGreen dsDNA Assay | Thermo Fisher | P11495 | dsDNA specific intercalator dye |
Quick Ligation kit | New England BioLabs | M2200L | T4 DNA ligase (NEB) |
RNaseOUT Recombinant Ribonuclease Inhibitor | Thermo Fisher | 10777019 | RNAse inhibitor |
S-4FB Crosslinker (DMF-soluble) | Vector laboratories | S-1004-105 | Succinimidyl 4-formylbenzoate (S-4FB) |
S-HyNic | Vector laboratories | S-1002-105 | Succinimidyl 6-hydrazinonicotinate acetone hydrazone (S-HyNic) |
Sodium Acetate, 3 M, pH 5.2, Molecular Biology Grade | MilliporeSigma | 567422-100ML | 3M Sodium acetate (pH 5.2) |
Sodium bicarbonate, 1M buffer soln., pH 8.5 | Alfa Aesar | J60408 | 1M sodium bicarbonate buffer, pH 8.5 |
Sodium phosphate dibasic for molecular biology | MilliporeSigma | S3264-250G | Na2HPO4 |
Sodium phosphate monobasic for molecular biology | MilliporeSigma | S3139-250G | NaH2PO4 |
SuperScript IV reverse transcriptase | Thermo Fisher | 18090050 | Reverse transcriptase |
SYBR Gold Nucleic Acid Gel Stain (10,000x Concentrate in DMSO) | Thermo Fisher | S11494 | An intercalator dye for DNA |
T4 DNA Ligase Reaction Buffer | New England BioLabs | B0202S | 10x T4 DNA ligase reaction buffer |
ThermoPol Reaction Buffer Pack | New England BioLabs | B9004S | 10x TPM-T buffer (Tris-HCl/Pottasium chloride/Magnesium sulfate/Triton X-100) |
TRIzol LS reagent | Thermo Fisher | 10296-028 | Guanidinium thiocyanate-phenol-chloroform extraction |
TruSeq Nano DNA library prep kit | Illumina | 20015965 | A DNA library preparation kit (see also the manufacturer's instruction) |
Ultramer DNA Oligo, Anti-5hmC_Ab#005 | Integrated DNA Technologies | N/A, see Table 3 | An amine-modified DNA probe for antibody |
Ultramer DNA Oligo, Anti-H3K27ac_Ab#002 | Integrated DNA Technologies | N/A, see Table 3 | An amine-modified DNA probe for antibody |
Ultramer DNA Oligo, Anti-H3K27me3_Ab#003 | Integrated DNA Technologies | N/A, see Table 3 | An amine-modified DNA probe for antibody |
Ultramer DNA Oligo, Anti-Med1_Ab#004 | Integrated DNA Technologies | N/A, see Table 3 | An amine-modified DNA probe for antibody |
Ultramer DNA Oligo, Anti-Pol II_Ab#006 | Integrated DNA Technologies | N/A, see Table 3 | An amine-modified DNA probe for antibody |
Ultramer DNA Oligo, Control IgG_Ab#001 | Integrated DNA Technologies | N/A, see Table 3 | An amine-modified DNA probe for control IgG |
UltraPure 0.5 M EDTA, pH 8.0 | Thermo Fisher | 15575020 | 0.5M EDTA, pH 8.0 |
UltraPure DNase/RNase-Free Distilled Water | Thermo Fisher | 10977023 | Ultrapure water |
Zeba Splin Desalting Columns, 7K MWCO, 0.5 mL | Thermo Fisher | 89882 | Desalting column |
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