In all experiments involving the use of yeast, lysis was performed using a mechanical bead
beating procedure in 1% SDS-containing buffer. In all HeLa, mESC, and NP experiments, lysis
was performed using 1% SDS-containing buffer with Benzonase treatment to shear chromatin.
Details of yeast, HeLa, mESC, and NP lysis, reduction, and alkylation protocols are given in the
Supplementary Information.
Drosophila embryos were lysed using a solution-based procedure with sonication.
Single embryos in PCR tubes were re-suspended in 20 μl of lysis buffer containing
20 μg of SP3 beads. Lysis buffer was composed of 1% SDS (Bio-Rad), 1×
cOmplete Protease Inhibitor Cocktail-EDTA (Roche), 5 mM EDTA, 5 mM EGTA, 10 mM
NaOH, and 10 mM DTT, in 10 mM HEPES buffer at pH 8.5 (Sigma). The lysis solution was
combined with 20 μl of neat trifluoroethanol (Sigma) and sonicated for 15 min
in a Bioruptor (Diagenode) for 10 cycles (30 s on, 30 s off) on the setting
‘high’. The Bioruptor was operated in the absence of active cooling to allow the water
bath to heat and facilitate lysis and shearing of chromatin. To neutralize the lysis solution,
0.75 μl of 0.1% formic acid was added. Samples were then heated at 95°C
for 5 min and placed on ice before proceeding with reduction and alkylation steps. (Details
of reduction and alkylation can be found in the Supplementary Information.)
beating procedure in 1% SDS-containing buffer. In all HeLa, mESC, and NP experiments, lysis
was performed using 1% SDS-containing buffer with Benzonase treatment to shear chromatin.
Details of yeast, HeLa, mESC, and NP lysis, reduction, and alkylation protocols are given in the
Supplementary Information.
Drosophila embryos were lysed using a solution-based procedure with sonication.
Single embryos in PCR tubes were re-suspended in 20 μl of lysis buffer containing
20 μg of SP3 beads. Lysis buffer was composed of 1% SDS (Bio-Rad), 1×
cOmplete Protease Inhibitor Cocktail-EDTA (Roche), 5 mM EDTA, 5 mM EGTA, 10 mM
NaOH, and 10 mM DTT, in 10 mM HEPES buffer at pH 8.5 (Sigma). The lysis solution was
combined with 20 μl of neat trifluoroethanol (Sigma) and sonicated for 15 min
in a Bioruptor (Diagenode) for 10 cycles (30 s on, 30 s off) on the setting
‘high’. The Bioruptor was operated in the absence of active cooling to allow the water
bath to heat and facilitate lysis and shearing of chromatin. To neutralize the lysis solution,
0.75 μl of 0.1% formic acid was added. Samples were then heated at 95°C
for 5 min and placed on ice before proceeding with reduction and alkylation steps. (Details
of reduction and alkylation can be found in the Supplementary Information.)
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