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Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging

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Abstract

Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal aberrant transcription initiation inside genes during senescence and aging that co-occurs with changes in the chromatin landscape. Interventions that alter these spurious transcripts have profound consequences on cellular health, primarily affecting intracellular signal transduction pathways. We propose that age-related spurious transcription promotes a noisy transcriptome and degradation of coherent transcriptional networks.

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Fig. 1: Cryptic TSSs are activated in proliferating and senescent cells.
Fig. 2: Chromatin acetylation profiles around cryptic TSSs suggest that H3K27ac drives cryptic transcription.
Fig. 3: Chromatin methylation profiles around cryptic TSSs suggest an enhancer-to-promoter conversion in senescent cells.
Fig. 4: Senescent-not-Proliferating cryptic TSSs lose DNA methylation in senescence.
Fig. 5: The AP1 family of pioneer factors drives the formation of cryptic TSSs.
Fig. 6: Aged mouse livers show evidence of intragenic cryptic transcription.

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Data availability

The GEO accession number for all genome-wide datasets generated in this article is GSE156829. The following publicly available datasets downloaded from the GEO and used in this study are:

1. Shah et al., 2013 – GSE36616

2. Cruickshanks et al., 2013 – GSE48580

3. Rai et al., 2014 – GSE56307

4. Sen et al., 2019 – GSE106146

5. Chan et al., 2022 – GSE175533

All image data have been deposited to Mendeley Data (https://doi.org/10.17632/mtns8fjk9w.1). See also Source Data (for qPCR analysis, western blot and microscopy images) accompanying this manuscript.

Code availability

All code used in this manuscript has been deposited to GitHub: https://github.com/gdonahue/Sen_NA_2022.

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Acknowledgements

We would like to thank K. Alexander and D. Mahat for PRO-seq/PRO-cap/ChRO-cap guidance and members of the Berger laboratory for critical reading of the manuscript. We would also like to thank D. Jha for insightful discussions. This work was supported by National Institutes of Health/National Institute on Aging grant P01AG031862 to S.L.B., American Heart Association grant 15POST21230000, AFAR Irene Diamond Transition Award DIAMOND 17113 and National Institute on Aging Intramural Research Program grant ZIA-AG-000679 to P.S.

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Author notes

  1. Payel Sen

    Present address: Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

  2. Neil Robertson & Peter D. Adams

    Present address: Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK

Authors and Affiliations

  1. Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA

    Payel Sen & Na Yang

  2. Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Greg Donahue, Catherine Li, Gabor Egervari, Yemin Lan, Parisha P. Shah, Erik Kerkhoven & Shelley L. Berger

  3. Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA

    Neil Robertson & Peter D. Adams

  4. High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA

    David C. Schultz

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Contributions

P.S. and S.L.B. conceptualized the work. P.S. generated most genome-wide datasets used in this study (except those already published, as indicated in Supplementary Table 2). C.L. performed functional experiments, such as qPCR detection of PRO-cap peaks and replicative senescence assays with cells overexpressing BATF. G.E. performed PRO-cap on cells overexpressing BATF. N.Y. helped in wet lab experiments. G.D., E.K. and Y.L. performed bioinformatics analyses of data. N.R. processed WGBS data, which were generated in the laboratory of P.D.A. D.C.S. provided concentrated lentiviral preparations used in this study. P.P.S. performed ATAC-seq and participated in discussions.

Corresponding authors

Correspondence to Payel Sen or Shelley L. Berger.

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Nature Aging thanks Jesus Gil and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information.

Supplementary Figure Legends 1–9, Supplementary Tables 1–4 (Supplementary Table 1 supplied as Supplementary Data), Supplementary Source Data, Supplementary References and Supplementary Figs. 1–9

Reporting Summary

Supplementary Table 1.

List of Proliferating-not-Senescent, Senescent-not-Proliferating, Young-not-Old and Old-not-Young peaks.

Source data

Source Data Fig. 1

qPCR raw data for Fig. 1i

Source Data Fig. 5

β-gal assay and EdU assay raw data and calculations for Fig. 5a,i

Source Data Fig. 5

Unprocessed western blot and EdU images for Fig. 5e,i

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Sen, P., Donahue, G., Li, C. et al. Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. Nat Aging 3, 402–417 (2023). https://doi.org/10.1038/s43587-023-00384-3

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