Mechanisms of Inherited Epigenetic Dysregulation in Early Embryonic Development

一波主要的重新编程浪潮重置了早期胚胎的全基因组DNA甲基化图谱。然而，我们最近发现的有限数量的重要序列和新区域必须避开这些动态变化，并通过持续的DNMT1(DNA甲基转移酶1)活性来维持精确的DNA甲基化。这些DNA甲基化标记的不忠实传递会导致遗传性表观遗传失调(表观遗传错误的细胞间传递)，这反过来可能是调控网络中发现异常背后的部分病因。*遗传性表观遗传失调是如何在失去依赖DNMT1的DNA甲基化维持后出现的？为了解决这个问题，我们建立了一个具有可诱导的DNMT1抑制的转基因胚胎干细胞模型，以重现胚胎的去甲基化和再甲基化波，而不需要任何DNMT1依赖的维持活性。*我们的主要假设：在早期胚胎计划中，表观遗传学图谱的失调将引发一系列特定的表观遗传学扰动，导致异常的表观遗传适应，从而阻止DNMT1维持图谱。使用下一代测序方法，我们将在我们创新的Dnmt1tet/Tet ES细胞模型中，建立DNA甲基化和组蛋白修饰的全面表观遗传学图谱，跨越DNA甲基化的丢失和恢复。*我们的三个目标是：*1-描述Dnmt1tet/tet ES细胞全基因组去甲基化和再甲基化过程中依赖DNMT1的DNA甲基化的动力学。通过建立DNMT1依赖的甲基化丢失和重建过程中全基因组DNA甲基化的动力学，我们将为清楚地理解遗传性表观遗传失调背后的机制奠定基础。*2-定义组蛋白表观遗传格局在完全丢失和重建依赖DNMT1的甲基化过程中的适应性反应。我们建议确定DNA甲基化图谱的暂时丢失是否触发特定组蛋白修饰中的永久性重排，这将阻碍结合因子在带有遗传性表观遗传失调的序列上招募DNMT1。*3-确定表观遗传格局中的特定适应是否阻止在诱导Dnmt1tet/tet ES细胞遗传失调后初始表观遗传学图谱的恢复。利用生物信息学，我们将交叉检查DNA甲基化(目标1)、组蛋白标记和相关DNA结合因子(目标2)的数据，以确定特定的表观遗传相互作用，解释遗传性表观遗传失调的机制。*我们的计划将回答有关胚胎细胞遗传性表观遗传失调的机械性问题，这些问题在其他系统中仍然难以捉摸，进一步建立了Dnmt1tet/tet ES细胞作为该领域的重要模型。

A major reprogramming wave resets genome-wide DNA methylation profiles in early embryos. However, a limited number of important sequences and novel regions that we recently identified must escape these dynamic changes and sustain precise DNA methylation profiles through continuous DNMT1 (DNA methyltransferase 1) activity. Unfaithful transmission of these DNA methylation marks leads to inherited epigenetic dysregulation (cell-to-cell transmission of epigenetic errors), which in turn could be part of the etiology behind abnormalities found in regulatory networks.***How does inherited epigenetic dysregulation emerges following a loss of DNMT1-dependent DNA methylation maintenance? To address this question, we developed a transgenic embryonic stem (ES) cell model with inducible Dnmt1 repression to reproduce the embryonic demethylation and remethylation waves without any DNMT1-dependent maintenance activity. ******Our main hypothesis: Dysregulation of epigenetic profiles in an early embryonic program will provoke a cascade of specific epigenetic perturbations, leading to abnormal epigenetic adaptation that prevents DNMT1 from maintaining profiles. Using next-generation sequencing approaches, we will establish comprehensive epigenetic maps for DNA methylation and histone modifications across the loss and regain of DNA methylation in our innovative Dnmt1tet/tet ES cell model. ******Our three aims are:***1- Delineate the kinetics of DNMT1-dependent DNA methylation throughout the process of genome-wide demethylation and remethylation in Dnmt1tet/tet ES cells. By establishing genome-wide DNA methylation dynamics during the loss and reestablishment of DNMT1-dependent methylation, we will set the foundation for a clear understanding of the mechanisms behind inherited epigenetic dysregulation.******2- Define the adaptive response in the histone epigenetic landscape during the course of complete loss and reestablishment of DNMT1-dependent methylation profiles. We propose to determine if temporary loss of DNA methylation profiles triggers permanent rearrangements in specific histone modifications that would impede binding factors to recruit DNMT1 on sequences bearing inherited epigenetic dysregulation.******3- Determine if specific adaptations in the epigenetic landscape prevent the recovery of initial epigenetic profiles following induced inherited dysregulation in Dnmt1tet/tet ES cells. Using bioinformatics, we will cross-examine data on DNA methylation (Aim 1), histone marks, and related DNA binding factors (Aim 2) to identify specific epigenetic interactions that explain mechanisms implicated in inherited epigenetic dysregulation. ******Our program will answer mechanistic questions about inherited epigenetic dysregulation in embryonic cells that have remained elusive in other systems, further establishing Dnmt1tet/tet ES cells as an important model in this field.********