Mechanisms of Inherited Epigenetic Dysregulation in Early Embryonic Development

一个主要的重编程浪潮重置了早期胚胎的全基因组DNA甲基化谱。然而，我们最近发现的有限数量的重要序列和新区域必须逃脱这些动态变化，并通过持续的DNMT1 （DNA甲基转移酶1）活性来维持精确的DNA甲基化谱。这些DNA甲基化标记的不忠实传递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的异常背后的病因学的一部分。

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.