Liu Y V, Suryatenggara J, Wong H, Jayasinghe M K, Tang J P, Tan H K, Kwon J, Zhou Q, Ummarino S, Ebralidze A K, Le M T N, Doench J G, Chai L, Benoukraf T, Hiwase D, Thomas D, Di Ruscio A, Tenen D G, Bassal M A
Cancer Science Institute of Singapore, 117599, Singapore.
Genetic Perturbation Platform, Broad Institute, Cambridge, MA 02142, USA.
Res Sq. 2024 Oct 16:rs.3.rs-4359582. doi: 10.21203/rs.3.rs-4359582/v1.
DNA methylation and mRNA expression correlations are often presented with inconsistent evidence supporting causal regulation. We hypothesized that causal regulatory methylation elements would exhibit heightened demethylation sensitivity. To investigate, we analyzed 20 whole-genomic bisulfite sequenced samples before and after demethylation and identified narrow-width (45-294 bp) elements within a short plateau, termed Methylation Mesa (MM). The Mesa signature was conserved across species and was independent of CpG islands. Mesa also demonstrate high concordance with primed and active histone marks. To assess causality, we developed CRISPR-DiR, a highly precise targeted demethylation technology. Targeted demethylation of a Mesa triggers locus and distal chromatin rewiring events that initiate mRNA expression significantly greater than promoter-CpG island targeting. Thus, Mesa are self-sustaining epigenetic regulatory elements that maintain long-term gene activation through focused demethylation only within the Mesa core, resulting in subsequent histone modifications and chromatin rewiring events that interact with distal elements also marked as Mesas.
DNA甲基化与mRNA表达的相关性常常呈现出支持因果调控的不一致证据。我们假设因果调控甲基化元件会表现出更高的去甲基化敏感性。为了进行研究，我们分析了20个全基因组亚硫酸氢盐测序样本在去甲基化前后的情况，并在一个短平台期内确定了狭窄宽度（45 - 294 bp）的元件，称为甲基化台地（MM）。台地特征在物种间是保守的，并且独立于CpG岛。台地还与引发和活跃的组蛋白标记高度一致。为了评估因果关系，我们开发了CRISPR - DiR，一种高度精确的靶向去甲基化技术。对台地的靶向去甲基化会触发基因座和远端染色质重塑事件，这些事件引发的mRNA表达显著高于靶向启动子 - CpG岛。因此，台地是自我维持的表观遗传调控元件，通过仅在台地核心内进行集中去甲基化来维持长期基因激活，从而导致随后的组蛋白修饰和染色质重塑事件，这些事件与也被标记为台地的远端元件相互作用。
