EXPERIMENT_TITLE: GSM4425983: HiC_Tween_rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 5-10 million cells were fixed in 1× phosphate buffered solution (PBS) with 2% formaldehyde for 10 minutes with occasional mixing. The reaction was quenched with by addition of 2 M glycine to a final concentration of 125 mM. Cells were pelleted by centrifugation (1,000 g, 10 minutes, 4 °C), resuspended in 50 μl of 1× PBS, snap-frozen in liquid nitrogen and stored at -80 °C. Cells were lysed in 1.5 ml of isotonic buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% (v/v) NP-40 substitute (Fluka), 1% (v/v) Triton-X100 (Sigma), 1× Halt™ Protease Inhibitor Cocktail (Thermo Scientific)) on ice for 15 minutes. Cells were pelleted by centrifugation at 2,500g for 5 minutes, resuspended in 100 μl of 1× DpnII buffer (NEB) and pelleted again. The pellet was resuspended in 200 μl of 0.3% SDS in 1.1× DpnII buffer and incubated at 37 °C for 1 hour. Then 330 μl of 1.1× DpnII buffer and 53 μl of 20% Triton X-100 (Sigma) were added, and the suspension was incubated at 37 °C for 1 hour. Next, 600 U of DpnII enzyme (NEB) were added, and the chromatin was digested overnight (14-16 hours) at 37 °C with shaking (1,400 rpm). In the morning, 200 U of DpnII enzyme were added and the cells were incubated for additional 2 hours. DpnII was then inactivated by incubation at 65 °C for 20 minutes. The nuclei were harvested for 10 minutes at 5,000 g, washed with 100 μl of 1× NEBuffer 2 and resuspended in 125 μl of 1.2× NEBuffer 2. Cohesive DNA ends were biotinylated by adding 25 μl of the biotin fill-in mixture (0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (NEB)). The samples were incubated at 37 °C for 75 minutes with shaking (1,400 rpm). Nuclei were pelleted by centrifugation at 3,000g for 5 minutes, resuspended in 300 μl of 1× T4 DNA ligase buffer (Fermentas) and pelleted again. The pellet was resuspended in 300 μl of 1× T4 DNA ligase buffer, and 75 U of T4 DNA ligase (Fermentas) were added. Chromatin fragments were ligated at 20 °C for 6 hours. The cross-links were reversed by overnight incubation at 65 °C in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation (glycogen (Thermo Scientific) at a concentration of 20 μg/ml was used as co-precipitator). After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl pH 8.0. To remove residual RNA, samples were treated with 50 μg of RNase A (Thermo Scientific) for 45 min at 37 °C. To remove residual salts and DTT, the DNA was additionally purified using Agencourt AMPure XP beads (Beckman Coulter). Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U of T4 DNA polymerase (NEB) in NEBuffer 2 supplied with 0.025 mM dATP and 0.025 mM dGTP at 20 °C for 4 hours. Next, the DNA was purified using Agencourt AMPure XP beads. The DNA was then dissolved in 500 μl of sonication buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.1% SDS) and was sheared to a size of approximately 100-1,000 bp using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified) using AMICON Ultra Centrifugal Filter Units to a total volume of about 50 μl. The DNA ends were repaired by adding 62.5 μl MQ water, 14 μl of 10× T4 DNA ligase reaction buffer (Fermentas), 3.5 μl of 10 mM dNTP mix (Fermentas), 5 μl of 3 U/μl T4 DNA polymerase (NEB), 5 μl of 10 U/μl T4 polynucleotide kinase (NEB), and 1 μl of 5 U/μl Klenow DNA polymerase (NEB) and incubating at 20 °C for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 μl 10× NEBuffer 2, 1.2 μl of 10 mM dATP, 1 μl of MQ water and 3.6 μl of 5 U/μl Klenow (exo-) (NEB). The reactions were carried out for 30 minutes at 37 °C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65 °C for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 200 μl of 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 10 μl of MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads with captured ligation junctions were resuspended in 50 μl of adapter ligation mixture composed of 41.5 μl MQ water, 5 μl 10× T4 DNA ligase reaction buffer (Fermentas), 2.5 μl of Illumina TruSeq adapters and 1 μl of 5 U/μl T4 DNA ligase (Fermentas). Adapter ligation was performed at 22 °C for 2.5 hours, and the beads were sequentially washed twice with 100 μl of TWB (5 mM Tris-HCl (pH 8.0), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl of 1× binding buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 2 M NaCl) and once with 100 μl of CWB (10 mM Tris-HCl (pH 8.0) and 50 mM NaCl) and then resuspended in 20 μl of MQ water. Test PCR reactions containing 4 μl of the streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles needed to generate enough PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98 °C, followed by 6, 9, 12, 15 and 18 cycles of 20 s at 98 °C, 15 s at 65 °C, and 20 s at 72 °C. The PCR reactions were separated on a 2% agarose gel supplied with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 12-15 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified using Agencourt AMPure XP beads.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)- mediated LLPS disruption/modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome clutches and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions and TAD insulation but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels. Overall design: This submission contains the following experiments on untreated (Control and Control_T), 1,6-hexanediol treated (Hex5), Tween-20 treated (Tween), 1,6-hexanediol treated + recovery (Recovery) and Tween-20 treated + recovery (Recovery_T) HeLa cells: 2 biological replicates of Hi-C in Control, Control_T, Hex5, Tween, Recovery and Recovery_T cells, 2 biological replicates of CTCF ChIP-seq in Control, Hex5 and Recovery cells.
SAMPLE_TITLE: HiC_Tween_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HiC_Tween"}, {"TAG": "cell line", "VALUE": "HeLa"}, {"TAG": "treatment", "VALUE": "Tween-20"}]
Pool_Member_@attributes_sample_title: HiC_Tween_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_Tween_rep1
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