Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RNA-seq]

Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. A cardiac-specific CTCF depletion model was used to examine how this protein maintains basal cardiac chromatin function and revealed that loss of CTCF causes widespread changes in accessibility and methylation that are distinct from those in pressure overload. Less than half of the gene expression changes occurring at either time point after pressure overload were explained by the actions of DNA methylation alone and accessibility was likewise an imperfect predictor of transcription. Distal enhancers were paired with genes based on chromatin structural data and the regulatory actions of these elements examined in the context of DNA methylation and accessibility: enhancer actions require specific combinations of transcription factors and histone modifications at different stages of disease and to execute a specific transcriptional event (methylation and accessibility alone were insufficient to predict the behavior). In summary, these studies characterize the logic employed at different coding, regulatory, and noncoding regions to regulate chromatin accessibility and transcription, providing a resource of epigenomic data at distinct temporal stages of heart failure. Overall design: Diferences in chromatin accessibility, DNA methylation and gene expression at early (3 days) and late (3 weeks) stage of cardiac disease, and during cardiac-specific CTCF depletion. TAC (transverse aortic constriction) samples represent mice with diseased hearts.

染色质修饰酶的调控可诱发或改善心力衰竭。鉴于众多染色质因子参与基因表达调控，我们在压力超负荷心肌肥厚的小鼠模型中，采用ATAC-seq（转座酶可及性测序）实时报告特定基因座的表观遗传修饰整体状态——即所有表观遗传修饰因子的总和。
在造模后3天的压力超负荷早期代偿阶段，染色质开放状态与DNA甲基化已出现广泛改变，其中大部分变化持续至失代偿阶段（造模后3周），这揭示了机体对病理刺激产生表观基因组代偿的时序特征。
我们采用心脏特异性CTCF（CCCTC结合因子）敲除模型，探究该蛋白如何维持心脏基础染色质功能，结果发现CTCF缺失引发的染色质开放状态与DNA甲基化改变，与压力超负荷模型中的变化存在显著差异。
压力超负荷造模后的两个时间点中，仅DNA甲基化调控无法解释超过半数的基因表达变化，染色质开放状态同样无法完美预测转录水平。
研究人员基于染色质结构数据，将远端增强子与靶基因进行关联，并结合DNA甲基化与染色质开放状态探究这些调控元件的作用机制：增强子发挥调控功能，需要不同疾病阶段的转录因子与组蛋白修饰形成特定组合，仅靠DNA甲基化与染色质开放状态不足以预测其调控行为。
综上，本研究阐明了心力衰竭不同时序阶段中，编码区、调控区与非编码区调控染色质开放状态与基因转录的内在逻辑，同时提供了心力衰竭不同时间节点的表观基因组数据资源。
整体实验设计：本研究检测了心脏疾病早期（造模后3天）与晚期（造模后3周）阶段，以及心脏特异性CTCF敲除过程中，染色质开放状态、DNA甲基化与基因表达的差异。TAC（横向主动脉缩窄，transverse aortic constriction）样本取自患病小鼠心脏。