Characterising novel regulators of TERRA R-loops

1 PhD project offered in the IPP summer call 2020

Scientific Background

Telomeres shorten upon each cell division and during organismal aging. The rate of telomere shortening and not the absolute length of telomeres has an important influence on lifespan. Organisms with fast rates of telomere shortening are generally short-lived, whereas those with slower rates of telomere attrition live longer. TERRA is a long non-coding RNA, which is transcribed from telomeres. TERRA has a strong tendency to from RNA-DNA hybrids (R-loops at telomeres). The TERRA R-loops can stimulate homology directed repair specifically at very short telomeres and this slows the rate of shortening and delays the onset of replicative senescence. The regulation of TERRA and TERRA R-loops may therefore have an important influence on rates of senescence and aging. At this stage, we still understand very little about how TERRA and its R-loops are regulated and this constitutes the basis of this project proposal.

PhD project proposal: Characterising novel regulators of TERRA R-loops

In collaboration with the lab of Falk Butter we have employed proteomic approaches to identify novel telomere binding proteins. Importantly, we determined that a large number of proteins associate to telomeres in an RNA dependent manner. Some of these proteins were found to specifically interact with telomeres in senescent cells where telomerase was not active and telomeres are short.
This project will focus on the novel proteins that we found telomere associated in an RNA dependent manner. We will use chromatin immunoprecipitation to verify the association of the proteins in vivo and see if the binding is dependent on RNA-DNA hybrids. We will investigate how deletion of the identified genes affects TERRA levels, R-loop levels and of course measure rates of telomere shortening during senescence. The project will use a mixture of genetic, biochemical and proteomic approaches with the end goal of learning more about how to regulate senescence and aging.

Relevant publications

Perez L, Özturk M, Butter F* and Luke B* (in press) Npl3 stabilizes R-loops at telomeres to regulate replicative senescence. EMBO Rep.

Niehrs C* and Luke B* (in press) R-loops as regulators of chromatin dynamics, transcription and genome integrity.Nature Reviews Molecular Cell Biology

Lockhart A, Pires V B, Bento F, Kellner V, Luke-Glaser S, Luke B (2019) RNase H1 and RNase H2 are differentially regulated to process RNA-DNA hybrids.Cell Reports, 10.1016/j.celrep.2019.10.108.

Graf M, Bonetti D, Lockhart A, Serhal K, Kellner V, Maicher A, Jolivet P, Teixeira M T, Luke B (2017) Telomere length determines TERRA and R-loop regulation through the cell cycle.Cell, 170: 72-85

Balk B*, Maicher A*, Klermund J, Luke-Glaser S, Dees M, Bender K and Luke B (2013) Telomeric RNA-DNA hybrids affect telomere length dynamics and senescence. Nature Structural & Molecular Biology, 20: 1199-1205.

Rippe K* and Luke B* (2015) TERRA and the state of the telomere. Nature Structural & Molecular Biology, 22: 853-858.


Brian Luke