Identifying mechanisms underpinning epigenetic homeostasis

PROJECT SUMMARY DNA methylation is important for gene regulation, transcriptional silencing of repetitive DNA and establishing genomic imprinting. While DNA methylation is a dynamic modification, which is added and removed by writer and eraser enzymes, it is faithfully inherited over many millions of cell divisions, and even evolutionary timescales. How these writers and erasers combine to ensure such accurate epigenetic inheritance is a critical question, as failure to accurately maintain DNA methylation patterns is associated with aging as well as numerous diseases, including cancers. Despite the importance of DNA methylation writers and erasers, the mechanisms that regulate and coordinate their genes to maintain epigenetic homeostasis remain poorly understood. A major goal of the Williams lab is to eliminate this gap in knowledge. Using the epigenetic model system Arabidopsis, which can tolerate loss-of-function mutations to all methylation writers and erasers, my lab will perform a comprehensive study of the gene regulatory mechanisms that regulate the expression of writer and eraser genes to ensure epigenetic homeostasis. This will include performing a mechanistic dissection of the cell-cycle regulation of genes encoding writer and eraser enzymes and their targeting by anciently conserved cell cycle transcription factors. Additionally, my lab seeks to identify new trans-acting factors involved in the regulation of epigenetic homeostasis by studying a naturally occurring strain of Arabidopsis with drastically different regulation of epigenetic modifiers. Lastly, my lab will precisely define how epigenetic homeostasis is lost within some cells during aging, identifying mechanisms that contribute to age-dependent DNA methylation losses, and determining how “epigenetic age” is influenced by organ regeneration and the environment. Together, these approaches will generate multiple insights into how DNA methylation dynamics are established at a cellular scale and coordinated to achieve epigenetic homeostasis. We anticipate that these findings will provide new insights into the laws of epigenetic stability and inheritance, which are crucial for understanding many aspects of the health of human cells.