Telomeres are nucleoprotein structures at the end of linear chromosomes and solve two fundamental challenges of linear genome organization: The incomplete replication of linear DNA ultimately leads to cellular senescence when one or a few telomeres reach a critically short length, a process termed ‘end replication problem’. Each cancer cell would also ultimately share this fate. However, they circumvent telomere shortening by one of two mechanisms: 85% of all tumors reactivate the expression of telomerase while the other 15 % use a recombination-based mechanism, termed Alternative Lengthening of Telomeres (ALT). In addition, the ‘end protection problem’ essentially leads to telomere-telomere fusions if telomeres are not efficiently hidden from recognition as double-stranded breaks. Both telomere shortening and deprotection may result in chromosomal fusions and subsequently breakage-fusion-bridge cycles that lead to telomere-driven genome instability. Through our expertise in quantitative proteomics we have identified several proteins that directly bind to telomeres and we are now studying how they contribute to telomere homeostasis and impact carcinogenesis.

Using a DNA pull-down assay based on in vitro reconstitution combined with quantitative mass spectrometry, we identified HOT1 as a direct telomere binding protein. In vivo, HOT1 acts as a dynamic telomere-binding protein with increased telomere association during active telomere elongation. In agreement with this, subsequent experiments have shown that HOT1 likely contributes to telomerase recruitment. We have since extended this approach and systematically investigated telomere-binding proteins in 16 vertebrate species, creating a phylointeractomics map of telomeres from zebrafish to human. Beyond known telomere-binding proteins, our screen discovered a series of zinc finger proteins, ZBTB48, ZNF524 and ZBTB10, that directly bind to telomeric DNA (and its variant sequences) through a conserved zinc finger motif. These proteins contribute to telomere homeostasis, e.g. ZBTB48 limits telomere elongation while ZNF524 supports telomere integrity. In addition, these proteins moonlight in non-telomeric functions, e.g. ZBTB48 also acts as a transcriptional activator by regulating chromatin accessibility at target promoters. We are now expanding our mechanistic understanding of these factors and their impact on chromatin organization, among others through in-house developed approaches interrogating chromatin compositions by quantitative mass spectrometry.