Menendez, J. (BMEB) – Resolving the variation and remodeling of human centromeres and telomeres with telomere-to-telomere genomes

Centromeres and telomeres are essential for chromosome stability, yet their highly repetitive sequences have historically limited study of their variation and dynamics. Centromeres direct kinetochore assembly on megabase-scale alpha-satellite (αSat) arrays, while telomeres protect chromosome ends. Both vary extensively between individuals and across cell divisions, developmental states, and disease. Long-read sequencing and complete telomere-to-telomere (T2T) assemblies now make these regions accessible. Centromere identity is specified epigenetically by the histone H3 variant CENP-A, which coincides with centromere dip regions (CDRs). CDRs are hypomethylated domains within active αSat arrays and can be detected from native long-read methylation. Telomere length also varies between chromosome ends. However, subtelomeric variation makes it difficult to assign telomeric reads to a chromosome end without an individual-specific assembly.

Building on haplotype-resolved near-T2T genomes from the Human Pangenome Reference Consortium (HPRC), the objective of this proposal is to develop long-read and pangenome-based tools that map kinetochore assembly sites and chromosome-end-specific telomeres. I will apply these tools across inheritance, population variation, cell-state transitions, and cancer. In Aim 1, I will use centrodip to identify CDRs from PacBio HiFi and ONT reads. I will track CDR stability across cell passaging and a three-generation pedigree, and define CDR variation across the HPRC. In Aim 2, I will develop pangenome-based tooling that assigns telomeric reads to chromosome ends with lr-giraffe. I will apply it to matched PBMCs, LCLs, and hiPSCs to trace changes in telomere length and telomere variant repeat (TVR) content across cell states. In Aim 3, I will annotate kinetochores and telomeres in six matched tumor/normal cell line pairs from the CASTLE panel. From these, I will define somatic centromeric and telomeric mutations and compare their variability to the baseline variation established in Aims 1 and 2. Together, this work will define how kinetochore assembly sites vary and are inherited across the human population. It will also define how centromeres and telomeres are remodeled by cancer and cell state. These tools will extend pangenome-scale analysis into the genome’s most repetitive regions, with implications for chromosomal instability, cancer, and aging.

Event Host: Julian Menendez, PhD Student, Biomolecular Engineering & Bioinformatics 

Advisor: Karen Miga

Zoom: https://ucsc.zoom.us/j/5047377540?pwd=Sb2mUlOcfQ5mX3T9TIDOMaeWvkfOR0.1&omn=92984500915

Passcode: 184739