Monitoring chromatin changes at telomeres during cellular aging

Supervisors: Helder Ferreira, Tom Owen-Hughes

Project Description:
The ends of linear chromosomes are capped by specialised protein-DNA structures termed telomeres which act to protect chromosome ends. Telomeres shorten every time cells replicate and are therefore strongly linked to cellular aging and senescence. After a certain period of time, telomeres become critically short. This activates a DNA damage response, resulting in cell cycle arrest and ultimately cell death (crisis). However, this telomere-imposed barrier is sometimes overcome by cells that then proliferate uncontrollably (survivor formation). Studying telomeres using standard DNA sequencing technologies has been challenging do to their highly repetitive DNA sequence. Consequently, they are commonly ignored during normal deep sequencing analyses. Therefore, we know relatively little about the underlying structural changes that occur at telomeres as cells progress through senescence and crisis. 

This project aims to overcome this difficulty by combining different next-generation DNA sequencing technologies. Using this, we will be able to follow detailed changes in telomere structure during normal and pathological aging in the simple model system budding yeast. Saccharomyces cerevisiae (budding yeast) is a genetically tractable model organism that has pioneered our understanding of chromatin structure and DNA repair pathways. Combining genome sequencing, ChIP-seq and RNA-seq, we will study yeast as they progress through cellular senescence, crisis and the establishment of survivors by deleting the telomerase enzyme (Est2). This work will help to address how cells maintain telomeres as part of healthy aging.

This project will apply the combined expertise of the Ferreira and Owen-Hughes labs. The Owen-Hughes lab has developed genomic approaches to study changes in chromatin structure (2). The Ferreira lab will apply molecular biology and genetics based approaches to study telomere behaviour (3). The student will receive training in a wide variety of skills including: molecular biology and cloning, yeast genetics and the generation and analysis of next-generation sequencing data.