Guerin Lindsey N, Scott Timothy J, Yap Jacqueline A, Johansson Annelie, Puddu Fabio, Charlesworth Tom, Yang Yilin, Simmons Alan J, Lau Ken S, Ihrie Rebecca A, Hodges Emily
Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
Biomodal, Chesterford Research Park, Cambridge CB10 1XL, UK.
Cell Rep. 2025 May 27;44(5):115680. doi: 10.1016/j.celrep.2025.115680. Epub 2025 May 9.
Chromatin and DNA modifications mediate the transcriptional activity of lineage-specifying enhancers, but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand this paradox, we established a highly resolved timeline of their dynamics during neural progenitor cell differentiation. We discovered that, while complete demethylation appears delayed relative to shorter-lived chromatin changes for thousands of enhancers, DNA demethylation actually initiates with 5-hydroxymethylation before appreciable accessibility and transcription factor occupancy is observed. The extended timeline of DNA demethylation creates temporal discordance appearing as heterogeneity in enhancer regulatory states. Few regions ever gain methylation, and resulting enhancer hypomethylation persists long after chromatin activities have dissipated. We demonstrate that the temporal methylation status of CpGs (mC/hmC/C) predicts past, present, and future chromatin accessibility using machine learning models. Thus, chromatin and DNA methylation collaborate on different timescales to shape short- and long-term enhancer regulation during cell fate specification.
染色质和DNA修饰介导了谱系特异性增强子的转录活性，但最近的研究对染色质可及性和DNA去甲基化是转录的先决条件这一教条提出了挑战。为了理解这一矛盾，我们建立了神经祖细胞分化过程中它们动态变化的高分辨率时间线。我们发现，虽然相对于数千个增强子寿命较短的染色质变化而言，完全去甲基化似乎延迟了，但DNA去甲基化实际上在观察到明显的可及性和转录因子占据之前就以5-羟甲基化开始了。DNA去甲基化的延长时间线造成了时间上的不一致，表现为增强子调控状态的异质性。很少有区域会获得甲基化，并且在染色质活性消散后很长时间，由此产生的增强子低甲基化仍然持续存在。我们证明，使用机器学习模型，CpG的时间甲基化状态（mC/hmC/C）可以预测过去、现在和未来的染色质可及性。因此，染色质和DNA甲基化在不同的时间尺度上协同作用，以塑造细胞命运决定过程中的短期和长期增强子调控。
