Center for Molecular Medicine Cologne

Andreas Beyer - C 04

Mechanisms of age-associated decline in splicing fidelity


The gradual decline of cellular functions is a major factor contributing to tissue degeneration and ageing associated diseases, such as chronic kidney disease. Despite its importance for many diseases, we lack understanding about the molecular mechanisms underlying such progressive functional loss. Clearly, improving our insight about the causes will help to develop preventative measures and possibly better treatments of common complex diseases.

Recent work by us and others has demonstrated that the age-associated decline of cellular functions is associated with the decline of RNA splicing fidelity.

We have shown that during ageing the speed of RNA Pol-II elongation increases, which leads to increased errors during transcription and splicing. Further, we could show that slowing down transcription improves the quality of transcripts and extends lifespan in different metazoan species. However, we lack understanding about the molecular factors contributing to this functional decline.

In this project we aim to (1.) identify tissue-specific and tissue-independent splicing ‘mistakes’ at high single-cell resolution, (2.) identify molecular co-factors improving or worsening splicing fidelity, and (3.) thus better understand effects of splicing fidelity on cellular fitness. We propose to tackle the above questions by performing extensive single-cell profiling in order to associate the emergence of specific splicing events with other molecular co-factors, such as the expression of splicing regulators, Pol-II components and chromatin regulators.

These experiments will be conducted in livers and kidneys from mice of different age and lifespan-extending interventions (dietary restriction). Importantly, we will employ innovative technologies that will allow us to profile chromatin states and RNA levels in the same cells, which will enable the direct correlation of chromatin state changes with splicing and gene expression changes. This project will heavily rely on single-cell bioinformatic methods developed in the Beyer lab.

Our Aims

  1. identify tissue-specific and tissue-independent splicing ‘mistakes’ at high single-cell resolution
  2. identify molecular co-factors improving or worsening splicing fidelity
  3. better understand effects of splicing fidelity on cellular fitness.

Previous Work

We have recently shown that an increase in RNA Pol-II elongation speed during ageing contributes to a decline of cellular and organismal fitness. Further, we and others (e.g. Heintz et al. 2017, Nature) have shown that transcript quality declines with age, including increasing numbers of splicing errors in nascent transcripts, the increased formation of circular RNAs, and increasing errors in the RNA sequence itself (mismatches with the DNA template).

We have also shown that lifespan extending interventions such as dietary restriction (DR) and genetically slowing down Pol-II elongation speed rescues these effects at least partially. We could show that slowing down Pol-II extends lifespan in worm and fly and it improved transcript quality, including reduced formation of (most likely) spurious exon-exon junctions.

  1. Debès C*, Leote AC*, Beyer A (2019) Computational approaches for the systematic analysis of ageing-associated molecular alterations (Review). Drug Discov. Tod.: Disease Mod. 27:51-59;
  2. Debès, […] Müller, […], Partridge, Beyer. Aging-associated changes in transcriptional elongation influence metazoan longevity. (In revision; pre-print available on bioRxiv
  3. Hahn O, […], Beyer A#, Partridge L#. (2018) Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity. PLoS Genet. 14(11):e1007766.
  4. Hahn O, […], Beyer A#, Reik W#, Partridge L# (2017) Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. Genome Biol. 18:56.
  5. Leote, Wu, Beyer (2019). Regulatory network-based imputation of dropouts in single-cell RNA sequencing data. (In revision; pre-print available at bioRxiv
  • Braun F, Rinschen M, Buchner D, Bohl K, Plagmann I, Bachurski D, Richard Spath M, Antczak P, Gobel H, Klein C, Lackmann JW, Kretz O, Puelles VG, Wahba R, Hallek M, Schermer B, Benzing T, Huber TB, Beyer A, Stippel D, Kurschat CE, and Muller RU (2020). The proteomic landscape of small urinary extracellular vesicles during kidney transplantation. Journal of extracellular vesicles 10, e12026.
  • Cappelletti V, Hauser T, Piazza I, Pepelnjak M, Malinovska L, Fuhrer T, Li Y, Dorig C, Boersema P, Gillet L, Grossbach J, Dugourd A, Saez-Rodriguez J, Beyer A, Zamboni N, Caflisch A, de Souza N, and Picotti P (2020). Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell 10.1016/j.cell.2020.12.021.
  • Charmpi K, Guo T, Zhong Q, Wagner U, Sun R, Toussaint NC, Fritz CE, Yuan C, Chen H, Rupp NJ, Christiansen A, Rutishauser D, Ruschoff JH, Fankhauser C, Saba K, Poyet C, Hermanns T, Oehl K, Moore AL, Beisel C, Calzone L, Martignetti L, Zhang Q, Zhu Y, Martinez MR, Manica M, Haffner MC, Aebersold R, Wild PJ, and Beyer A (2020). Convergent network effects along the axis of gene expression during prostate cancer progression. Genome biology 21, 302.
  • Johnsen M, Kubacki T, Yeroslaviz A, Spath MR, Morsdorf J, Gobel H, Bohl K, Ignarski M, Meharg C, Habermann B, Altmuller J, Beyer A, Benzing T, Schermer B, Burst V, and Muller RU (2020). The Integrated RNA Landscape of Renal Preconditioning against Ischemia-Reperfusion Injury. J Am Soc Nephrol 31, 716-30.
  • Kamrad S, Grossbach J, Rodriguez-Lopez M, Mulleder M, Townsend S, Cappelletti V, Stojanovski G, Correia-Melo C, Picotti P, Beyer A, Ralser M, and Bahler J (2020). Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance. Mol Syst Biol 16, e9270.
Prof. Dr. Andreas Beyer CMMC Cologne
Prof. Dr. Andreas Beyer

CECAD Cologne / RG location

Principal Investigator - C 04

Publications - Andreas Beyer

Link to PubMed

Figure 1