How genome-wide nucleosome loss reprograms transcription

• Applicant: Professor Dr. Felix Müller-Planitz
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry ; Cell Biology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 574508191

Nucleosomes regulate transcription, yet during natural ageing, they become substantially depleted across the genome in diverse organisms—including humans. This widespread nucleosome loss raises a key question: how does the transcription machinery cope with such loss? Promoter regions will become more broadly accessible when nucleosomes are lost, potentially triggering faster initiation. However, transcription factors may become limiting when many promoters compete simultaneously. Moreover, widespread activation of non-coding antisense transcription could interfere with canonical transcription, e.g. through polymerase collision. Likewise, one might expect elongation rates to increase in nucleosome-depleted chromatin. That is, unless of course nucleosomes do not represent substantial barriers to RNA Polymerase II (Pol II) progression in vivo at all, because histone chaperones and nucleosome remodeling enzymes keep nucleosomes sufficiently dynamic. Alterations in initiation and elongation kinetics that occur in response to nucleosome loss can directly impact transcript abundance and fidelity, co-transcriptional splicing, polyadenylation site selection, and mRNA stability—factors that influence cellular fitness and contribute to age-associated pathologies. It is therefore important to apply sensitive and quantitative strategies that map initiation and elongation kinetics in vivo. Here, we aim to quantitatively determine how acute nucleosome depletion reprograms transcription kinetics using Saccharomyces cerevisiae as a model. A robust nucleosome depletion protocol exists for yeast. Depletion mimics the degree of nucleosome loss observed in aged cells. Through an integrated strategy combining multiple genomics technologies, we will quantify changes in transcription initiation and elongation rates at genome-wide resolution. We thereby visualize how the nucleosome loss rewires the transcription program. To shed light on the mechanisms how nucleosome loss rewires transcription kinetics, we will map nucleosome architecture before and after nucleosome depletion using Fiber-seq, a cutting edge long-read nucleosome footprinting technology. We can then integrate Fiber-seq information with the transcription kinetic data, with the ultimate goal to construct predictive models linking nucleosome loss to transcriptional rewiring. The datasets will thus help establish a quantitative foundation for understanding nucleosome-mediated gene regulation with direct relevance to ageing research.

• DFG Programme: Research Grants