Unraveling the Telomere Black Box: A New Single-Molecule Approach to Define the Telomere Chromatin Landscape and its Functional Mechanisms

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Summary Telomeres are end-capping protein-DNA structures at the ends of the linear human chromosomes. They protect our genome integrity by sacrificing their repetitive DNA when the ends of the chromosome suffer attrition during DNA replication and camouflaging the chromosome ends from wrong DNA breakage recognition. Deregulation or loss of telomeres results in genome instability and leads to human diseases such as cancer and premature aging. The telomere's repetitive DNA nature provides a unique challenge in understanding their biological processes. This is because telomeric proteins can bind the repetitive telomeric DNA in many ways, leading to complexity and diversity in the telomere chromatin landscape; there are functional consequences to how telomeric proteins decorate a telomere chromatin landscape because these proteins directly participate in telomere protection and length maintenance. Thus, our understanding of telomeres is like a "black box". We know the inputs (proteins and lncRNA) and outputs (telomere length and end-protection) and understand how variations of inputs transform to output changes. However, we do not know what is going on inside the "black box". This "black box" is the telomere chromatin landscape. Characterizing the telomere chromatin landscape has been an insurmountable task for the telomere research field for decades. The ChIP-Seq technique has revolutionized chromosome biology research, but repetitive genomic regions such as the telomeres are left behind. This is because the relative positional information of the protein-DNA interactions is lost upon the fragmentation step in ChIP-Seq, preventing us from reconstructing the chromatin landscape of interest. This proposal seeks to innovate new tools to map the human telomere chromatin landscape at a single-telomere level. These tools will then use to study how the telomere chromatin landscape regulates telomere end-protection and length maintenance. First, I will establish the proof-of-concept experiments for using non-native DNA methylation to mark protein-DNA interactions at the repetitive telomeric DNA regions and reconstruct the chromatin landscapes with structural details. These tools will then be used to tackle two major research areas: (1) What is the human telomere chromatin landscape and how it changes across the cell cycle from a resting protective state to one permissive to DNA replication progression. (2) How changes in the human telomere chromatin landscape drive telomere length maintenance. This proposal thus consists of both technological and conceptual innovations. The new tools will provide a new way to investigate chromosome biology at repetitive genomic DNA regions; thus, its impact extends beyond the telomeres. We will get an unprecedented first look into the telomere chromatin landscape. Hence, this proposal has enormous potential to open multiple new research directions in telomere biology; a paradigm shift in our telomere knowledge is expected. Because of the biomedical importance of telomeres, the outcome of this proposal can provide novel avenues to tackle telomere-related human diseases.