Universität zu Köln

Papadakis, Antonios ORCID: 0000-0002-2416-6772 (2024). Aging associated changes of transcriptional elongation speed and transcriptional error rate. PhD thesis, Universität zu Köln.

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Abstract

Aging organisms show a pervasive decline in cellular function, with important implications for healthspan and lifespan. Aging associated impairment of gene transcription from Pol II are believed to underlie a large part of this phenotype. Elongation is a particularly important step of transcription since it regulates a lot of cotranscriptional processes, however the exact molecular mechanisms involved in its changes with aging remain unclear. In this thesis, we report the effects of aging in various transcriptional processes across different eukaryotes. We use a combination of previously published and newly-generated next generation sequencing data to understand the mechanisms of aging associated changes in Pol II speed and fidelity We profiled and analyzed genome-wide, aging-related changes in transcriptional processes across different organisms: nematode worms, fruit flies, mice, rats and humans. The average transcriptional elongation speed (Pol II speed) increased with age in all five species. Along with these changes in elongation speed, we observed changes in co-transcriptional processes that are partially regulated by elongation, including splicing alterations, the formation of more circular RNAs and loss of transcriptional fidelity. Two lifespan-extending interventions, dietary restriction and lowered insulin/Igf signaling, both partially reversed some of these aging-related changes. Remarkably, genetic variants of Pol II that reduced its speed in worms and flies increased their lifespan, which proves the importance of elongation rate for organismal longevity. Similarly, reducing Pol II speed by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal aging and lifespan-extending interventions, and point to possible preventative measures. Furthermore, we developed a new computational pipeline, scErrorRate, that utilizes UMI-based single-cell data to estimate transcriptional error rate. It is a computational approach that does not require the onerous process of rolling circle-based technologies. Using scErrorRate, we were able to profile the error spectrum of Pol II in mice and human cell culture. For the first time, we characterized changes in transcriptional fidelity caused by aging and senescence, showing an overall increase in transcriptional misincorporations. Taken together, this work provides new insight on the fundamental molecular mechanisms underlying aging.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Papadakis, Antonios UNSPECIFIED orcid.org/0000-0002-2416-6772 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-721595
Date:	2024
Place of Publication:	Cologne
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	CECAD - Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language Pol-II, RNA-Seq, transcriptomics, transcriptional speed, transcriptional fidelity English
Date of oral exam:	13 February 2023
Referee:	Name Academic Title Gehring, Niels Prof. Dr
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/72159