Pamela Milani (Fraenkel Lab) pmilani@mit.

edu Jan 2016

Assay for Transposase Accessible Chromatin using Sequencing

(ATAC-Seq)

Protocol modified from:

Transposition of native chromatin for fast and sensitive epigenomic profiling of open
chromatin, DNA-binding proteins and nucleosome position. (Buenrostro et al., Nat Methods.
2013 Dec;10(12):1213-8).
Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced
pluripotent stem cells. (Milani et al., Scientific Reports 6, Article number: 25474 (2016)).

Overview of the protocol and QC

ATAC-Seq detects open-chromatin regions and maps transcription factor binding events genome-
wide by means of direct in vitro transposition of native chromatin. Specifically, hyperactive Tn5
transposase is used to interrogate chromatin accessibility by inserting high-throughput DNA
sequencing adapters into open genomic regions, which allows for the preferential amplification
of DNA fragments located at sites of active chromatin.
The ATAC-Seq protocol was adapted from Buenrostro et al. (2013), with some modifications.
Given that a successful ATAC-Seq experiment begins with the isolation of high-quality intact
nuclei, we have first introduced a quality control checkpoint consisting of the morphological
evaluation of nuclei with either Trypan Blue or DAPI staining, followed by the accurate
quantification of those nuclei using an automated cell counter. Precise counting of nuclei is
important to ensure optimal tagmentation (the simultaneous fragmenting of the DNA and
insertion of adapter sequences) and to limit the technical variability across samples. From a
qualitative perspective, individual intact nuclei with a round or oval shape should be observed
with no visible clumping. To exclude samples with severe degradation or over-tagmentation, we
assess the quality of the treated chromatin samples by gel electrophoresis, as described in
Buenrostro et al. (2013); if the chromatin was intact and the transposase reaction was optimal, a
 Pamela Milani (Fraenkel Lab) [email protected] Jan 2016

DNA laddering pattern with a periodicity of about 200bp should be observed, corresponding to
fragments of DNA that were originally protected by an integer number of nucleosomes
(nucleosome phasing). Furthermore, we measure the enrichment of DNA accessible regions by
performing real-time qPCR analysis using a known open-chromatin site as a positive control and
a Tn5-insensitive site as a negative control. When assayed by real-time qPCR, high-quality ATAC-
Seq samples should show at least a 10-fold enrichment of positive control sites compared to
Tn5-insensitive sites. Finally, as we are principally interested in open-chromatin profiling and not
in nucleosome positioning, we have introduced a size-selection step to enrich for nucleosome-
free fragments. This step increases the signal-to-noise ratio and improves the sensitivity of the
methodology. After size-selection, libraries are PCR-amplified and submitted for single-end
sequencing. Figure 1 shows the outline of ATAC-Seq procedure.

Figure 1. Outline of ATAC-Seq key experimental steps and quality control (QC) checkpoints.

Materials and equipment:

Agencourt AMPure XP (5 mL), Beckman Coulter, cat #: A63880

cOmplete Protease Inhibitor Cocktail Tablets EDTA-free, Sigma-Aldrich, cat #: 11873580001
Countess Cell Counting Chamber Slides, Thermo Fisher Scientific, cat #: C10228
Countess II FL Automated Cell Counter, Thermo Fisher Scientific, cat #: AMQAF1000
 Pamela Milani (Fraenkel Lab) [email protected] Jan 2016

CryoStor CS10, Stemcell Technologies, cat #: 07930

DNA Clean & Concentrator 5 Kit, Zymo Research, cat #: D4013
DR88M transilluminator package, Clare Chemical Research
E-Gel EX Agarose Gels, 2%, Thermo Fisher Scientific, cat #: G4020-02
E-Gel iBase and E-Gel Safe Imager Combo Kit, Thermo Fisher Scientific, cat #: G6465
E-Gel50 bp DNA Ladder, Thermo Fisher Scientific, cat #: 10488-099
Elution Buffer (EB) (10 mM TrisCl, pH 8.5), Qiagen, cat #: 19086
Ethanol, Pure, 200 Proof (100%), KOPTEC, VWR, cat #: 71001-862
KAPA SYBR FAST qPCR Master Mix, (5 mL), Kapa Biosystems, cat #: KK4601
Magnetic stand for PCR tubes
Mr. Frosty Freezing Container, Thermo Fisher Scientific, cat #: 5100-0001
NEBNext High-Fidelity 2X PCR Master Mix, New England Biolabs, cat #: M0541S
Nextera DNA Sample Preparation Kit (24 samples), Illumina, cat #: FC-121-1030
Nextera Index Kit (24 indexes, 96 samples), Illumina, cat #: FC-121-1011
Nuclease-Free Water, Integrated DNA Technologies, cat #: 11-05-01-14
Single-edge industrial razor blades, VWR, cat #: 55411-050
Thermal Cycler
Zymoclean Gel DNA Recovery Kit, Zymo Research, cat #: D4007

Procedure

I. Cell Preparation and Nuclei Isolation

1. Wash the cells once or twice with 1X PBS, isolate them via cell scraper in 1X PBS, and
centrifuge at 250 rcf for 5 min at 4C.
2. Cryopreservation: aspirate the supernatant, resuspend the pellets in Cryostor media, transfer
the cell suspension to cryovials and freeze slowly in a Mr. Frosty Freezing Container (Thermo
Fisher Scientific), filled with isopropyl alcohol, at -80C.
 Pamela Milani (Fraenkel Lab) [email protected] Jan 2016

3. Thawing: remove the cryovials from -80C and quickly warm them for 2 min in a 37C water
bath. Transfer the samples to 12 ml of warm 1X PBS supplemented with 1X protease inhibitor
cocktail. Gently mix each tube by inversion and centrifuge at 250 rcf for 5 min at 4C. Carefully
aspirate the supernatant and proceed with nuclei isolation.
4. Nuclei isolation: gently resuspend the cell pellet in 100 L of ice-cold lysis buffer (10 mM Tris-
HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630*, 1X protease inhibitor cocktail).
Transfer the cell suspension to 0.2 ml tubes and incubate on ice for 5 min. Spin down at 250
rcf for 5 min at 4C.
5. Carefully discard the supernatant and resuspend the nuclear pellet in 20 L of ice-cold 1X TD
buffer (diluted from 2X TD buffer (Illumina, FC-121-1011) with ultrapure nuclease-free water)
6. Take 2 L of nuclear suspension and dilute 1:5 by adding lysis buffer (without IGEPAL). Add
10 L of Trypan Blue Solution (Thermo Fisher Scientific) and count the nuclei with the
Countess II FL Automated Cell Counter (Thermo Fisher Scientific), according to
manufacturers instruction. Calculate the number of nuclei/L.
7. QC checkpoint: inspect the nuclei by light microscopy; high-quality nuclei should be intact
with round or oval shape and no clumping should be observed, as shown in Figure 2 (sample
on the left).

Figure 2. Nuclear morphological evaluation: the nuclei on the left are of high quality, while excessive
clumping is observed for the nuclei on the right.

*Note: the optimal concentration of IGEPAL CA-630 to achieve maximal cell lysis without nuclear damage must
be determined empirically for each specific cell type.

II. Transposition Reaction and Purification

 Pamela Milani (Fraenkel Lab) [email protected] Jan 2016

1. Ensure that the nuclei are set on ice and prepare the transposition reaction mix as indicated
below (final volume = 50 L):

25 x/2 L 2X TD buffer (Illumina, FC-121-1011)

22.5 x/2 L ultrapure water
x L nuclei (previously resuspended in 1X TD buffer total number = 50,000)
2.5 L TDE1 (Tagment DNA Enzyme Illumina, FC-121-1011)

4. Gently pipette to resuspend the nuclei in the transposition reaction mix.

5. Incubate the transposition reaction mix at 37C for 30 min (in the thermal cycler).
6. Immediately following transposition, purify using a DNA Clean & Concentrator 5 Kit (Zymo
Research) according to the manufacturers protocol. Elute the DNA with 21 L of Elution Buffer
(Qiagen).
7. Store 10 L of purified transposed DNA at -20C for possible future usage.
8. Use the remaining 10 L for PCR reaction (PCR amplification (8 cycles) step).

III. PCR amplification (8 cycles)

1. To amplify transposed DNA fragments, combine the following in a PCR tube (final volume =
50 L):

15 L Nextera PCR Master Mix (NPM Illumina, FC-121-1011)

5 L PCR Primer Cocktail (PPC Illumina, FC-121-1011)
5 L Index primer 1 (i7 Illumina, FC-121-1011)
5 L Index primer 2 (i5 Illumina, FC-121-1011)
10 L Ultrapure nuclease-free water
10 L Transposed DNA

2. Perform PCR using the following program on a thermal cycler (Note: ensure that the thermal
cycler lid is heated during the incubation):
 Pamela Milani (Fraenkel Lab) [email protected] Jan 2016

72C for 3 minutes

98C for 30 seconds
8 cycles of:
98C for 10 seconds
63C for 30 seconds
72C for 3 minutes
Hold at 4C

3. Purify using DNA Clean & Concentrator 5 Kit (Zymo Research) according to the
manufacturers protocol. Elute the DNA with 21 L Elution Buffer (Qiagen).

IV. Gel-based qualitative evaluation of libraries and size selection

1. Load 20 L of purified PCR reaction from step III.3 on E-Gel EX Agarose Gels, 2% (Thermo
Fisher Scientific). Load also 4 L of E-Gel50 bp DNA Ladder (Thermo Fisher Scientific) diluted
with ultrapure water to a final volume of 20 L.
2. Run for 10 min using the pre-set E-Gel EX program on the E-Gel iBase Power System
(Thermo Fisher Scientific).
3. QC checkpoint: high-quality ATAC-Seq libraries should display clear nucleosome phasing, as
shown in Figure 3 (sample on the left).

Figure 3. The sample on the left passed the QC checkpoint, while the sample on the right shows DNA
smearing on the gel, likely caused by sample degradation.
 Pamela Milani (Fraenkel Lab) [email protected] Jan 2016

4. Using the DR88M transilluminator and a clean razor blade, size select 175 - 250 bp (fraction
A, corresponding to a nucleosome-free fragment size) and 250 - 625 bp (fraction B).
5. Purify the DNA from both gel fractions using the Zymoclean Gel DNA Recovery Kit (Zymo
Research), following the manufacturers recommendation, and elute the DNA with 22 l of
Elution Buffer (Qiagen).
6. QC checkpoint: use the DNA from fraction B for qPCR-based qualitative analysis of libraries
with primers mapping to open-chromatin regions as positive control sites and gene desert
regions as negative control sites (Figure 4). Perform the qPCR assay also using non-transposed
genomic DNA as a template to correct for any difference in primer efficiency. Prepare the
amplification reaction with KAPA SYBR FAST qPCR Master Mix (Kapa Biosystems) and forward
and reverse primers (500 nM final concentration). Calculate the fold enrichment of the open-
chromatin site (OC) over the Tn5-insensitive site (INS) with the following formula:
Fold Enrichment (FE) = 2[(OCg-OCa) - (INSg-INSa)]
where OCg is the qPCR threshold cycle number obtained for the OC qPCR primer pair using
non-transposed genomic DNA as template, and INSa is the qPCR threshold cycle number
obtained for the INS qPCR primer pair using ATAC-Seq library as template.

Figure 4. Sequences and genomic locations, displayed on the UCSC Genome Browser, of the primers
used to amplify positive (human GAPDH gene promoter) and negative (human gene desert region)
control sites.

V. Final amplification
1. Combine the following reagents in a PCR tube (final volume = 50 L):
 Pamela Milani (Fraenkel Lab) [email protected] Jan 2016

- 20 L size-selected DNA (fraction A = nucleosome-free fragments)

- 3 L Nuclease Free water
- 1 L 10 M PCR Primer IS5 (PAGE or HPLC purified)
- 1 L 10 M PCR Primer IS6 (PAGE or HPLC purified)
- 25 L NEBNext High-Fidelity 2x PCR Master Mix

IS5 (reamp.P5) 5'-A*ATGATACGGCGACCACCG*A

IS6 (reamp.P7) 5'-C*AAGCAGAAGACGGCATACG*A

2. Perform PCR using the following program on a thermal cycler (Note: make sure that the
thermal cycler lid is heated during the incubation):

98C for 30 seconds

5-7* cycles of
98C for 10 seconds
65C for 30 seconds
72C for 30 seconds
72C for 5 minute
Hold at 4C

* Note: optimize the number of cycles to avoid saturation in order to reduce GC and size bias.

3. Use AMPure XP beads (50 l) to purify the DNA following the manufacturers instruction.
4. Store 10 L at -20C and submit 10 L for quality control (BioAnalyzer and qPCR) and
sequencing (Illumina HiSeq2000).