Table 3. Techniques to study epigenetic regulation during cell cycle transition.
Table summarizing current methods to isolate cells in different phases of the cell cycle, study chromatin dynamics after DNA replication, or conditionally perturb epigenetic regulators.
| Method | Application | Ref. | |
| Cell cycle phase isolation | Chemical agents | ||
| Mimosine | Arrest cells in late G1 | (230) | |
| Thymidine | Arrest cells in S phase | (203) | |
| Aphidicolin | Arrest cells in early S phase | (231) | |
| Hydroxyurea | Arrest cells in early S phase | (232) | |
| RO-3306 | Arrest cells in G2-M phase | (233) | |
| Nocodazole | Arrest cells in prometaphase. Usually combined with mitotic shake-off | (204) | |
| Colcemid | Arrest cells in metaphase | (234) | |
| Drug-free | |||
| Serum starvation | Arrest cells at G0/G1 phase | (235) | |
| Centrifugal elutriation | Centrifugation-based separation of asynchronous populations in G1, S, and G2 fractions | (205) | |
| FUCCI | Fluorescence-based separation of asynchronous populations in G1, S, and G2 fractions | (206) | |
| Vybrant DyeCycle | Fluorescence-based separation of asynchronous populations in G1, S, and G2 fractions | (236) | |
| S-phase chromatin dynamics | DNA methylation | ||
| Repli-BS | Measures DNA methylation on newly synthesized daughter strands | (97) | |
| nasBS-seq | Measures DNA methylation in a strand-specific fashion on newly synthesized DNA | (237) | |
| Hammer-seq | Measures the methylation status of both strands on newly synthesized DNA within the same molecule | (23) | |
| iDEMS | Measures DNA modifications on metabolically labeled DNA by mass spectrometry | (139) | |
| Chromatin factors | |||
| NCC + tripleSILAC | Measures the composition of nascent chromatin on newly replicated DNA by mass spectrometry | (238) | |
| ChOR-seq | Measures chromatin factor binding on nascent chromatin after DNA replication | (208) | |
| SCAR-seq | Measures chromatin factor binding on nascent chromatin of sister chromatids after DNA replication | (208) | |
| CRISPR-biotinylation | Tracks the parental nucleosome localization after DNA replication in a locus-specific manner | (117) | |
| CUT&FLOW | Measures chromatin factor binding by CUT & Tag in nuclei sorted in cell cycle fractions by flow cytometry | (141) | |
| Conditional perturbation | Degrons | ||
| Auxin-inducible | Allows rapid degradation of the protein of interest upon addition of auxin-family plant hormones | (211) | |
| dTAGs | Allows rapid degradation of the protein of interest upon addition of the dTAG | (212) | |
| Cyclin B | Temporal loss of function of the protein of interest during M-to-G1 transition | (150) | |
| Light-inducible | Controls the expression of the protein of interest in a tight spatial and temporal manner | (239) | |
| Inhibitors | |||
| EZH2 inhibitors | Inhibits EZH2 methyltransferase activity | (213) | |
| RB-3 | Inhibits recruitment of RING1B to chromatin | (240) | |
| Chaetocin | Inhibits SUV39H1 and G9a methyltransferase activity | (214) | |
| UNC0638 | Inhibits GLP and G9a methyltransferase activity | (215) | |
| Hypomethylating agents | Nucleoside analogs (i.e. decitabine or azacytidine) that irreversibly inhibit DNMT1, 3A and 3B | (241, 242) | |
| GSK-3482364 | Selective, reversible, and non-covalent inhibitor of DNMT1 | (243) | |
| GSK-3685032 | Selective, reversible, and non-covalent inhibitor of DNMT1 | (216) | |