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A TORC1-histone axis regulates chromatin organisation and non-canonical induction of autophagy to ameliorate ageing

Lu, Yu-Xuan, Regan, Jennifer C, Eßer, Jacqueline, Drews, Lisa F, Weinseis, Thomas, Stinn, Julia, Hahn, Oliver, Miller, Richard A, Grönke, Sebastian, Partridge, Linda·2021·eLife

Abstract

Age-related changes to histone levels are seen in many species. However, it is unclear whether changes to histone expression could be exploited to ameliorate the effects of ageing in multicellular organisms. Here we show that inhibition of mTORC1 by the lifespan-extending drug rapamycin increases expression of histones H3 and H4 post-transcriptionally through eIF3-mediated translation. Elevated expression of H3/H4 in intestinal enterocytes in Drosophila alters chromatin organisation, induces intestinal autophagy through transcriptional regulation, and prevents age-related decline in the intestine. Importantly, it also mediates rapamycin-induced longevity and intestinal health. Histones H3/H4 regulate expression of an autophagy cargo adaptor Bchs (WDFY3 in mammals), increased expression of which in enterocytes mediates increased H3/H4-dependent healthy longevity. In mice, rapamycin treatment increases expression of histone proteins and Wdfy3 transcription, and alters chromatin organisation in the small intestine, suggesting that the mTORC1-histone axis is at least partially conserved in mammals and may offer new targets for anti-ageing interventions.

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  • Aging relies on the integration of cell-autonomous and non-cell-autonomous mechanisms.

    “This type of experiment demonstrates that aging relies on the integration of cell-autonomous and non-cell-autonomous mechanisms”

    From Hallmarks of aging: An expanding universe (2023) · cites this paper as [52]

    The Results section reports that changing histone expression specifically in fly enterocytes affected intestinal stem-cell proliferation and whole-fly lifespan, supporting a link between changes within cells and effects beyond those cells. The paper does not establish the broader claim that ageing generally relies on the integration of cell-autonomous and non-cell-autonomous mechanisms. No page numbers are available in our copy. (LLM, conf=0.78)

    Experimental — accuracy not yet measured
  • Increased histone expression extends lifespan in Drosophila.

    “Increased histone expression extends lifespan in Drosophila 52 , while increased histone H4K16 acetylation or H3K4 trimethylation, and decreased levels of H3K9 or H3K27 trimethylation are found in fibroblasts from aged individuals and progeroid patients.”

    From Hallmarks of aging: An expanding universe (2023) · cites this paper as [52]

  • Increasing autophagy solely in enterocytes of the intestine increases Drosophila lifespan.

    “For example, increasing autophagy solely in the enterocytes of the intestine increases Drosophila lifespan 52 .”

    From Hallmarks of aging: An expanding universe (2023) · cites this paper as [52]

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Research works printed but not linked: 79

  1. Alic, 2011, Death and dessert: nutrient signalling pathways and ageing, Current Opinion in Cell Biology, 23, 738, 10.1016/j.ceb.2011.07.006 · DOI
  2. An, 2017, Epigenetic regulation of starvation-induced autophagy in Drosophila by histone methyltransferase G9a, Scientific Reports, 7, 10.1038/s41598-017-07566-1 · DOI
  3. Arriola Apelo, 2016, Rapamycin: an InhibiTOR of aging emerges from the soil of easter island, The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, 71, 841, 10.1093/gerona/glw090 · DOI
  4. Benayoun, 2015, Epigenetic regulation of ageing: linking environmental inputs to genomic stability, Nature Reviews Molecular Cell Biology, 16, 593, 10.1038/nrm4048 · DOI · Paper page
  5. Biteau, 2008, JNK activity in somatic stem cells causes loss of tissue homeostasis in the aging Drosophila gut, Cell Stem Cell, 3, 442, 10.1016/j.stem.2008.07.024 · DOI · Paper page
  6. Biteau, 2010, Lifespan extension by preserving proliferative homeostasis in Drosophila, PLOS Genetics, 6, 10.1371/journal.pgen.1001159 · DOI
  7. Bjedov, 2010, Mechanisms of life span extension by rapamycin in the fruit fly Drosophila melanogaster, Cell Metabolism, 11, 35, 10.1016/j.cmet.2009.11.010 · DOI · Paper page
  8. Bolukbasi, 2017, Intestinal fork head regulates nutrient absorption and promotes longevity, Cell Reports, 21, 641, 10.1016/j.celrep.2017.09.042 · DOI
  9. Broer, 2015, GWAS of longevity in CHARGE consortium confirms APOE and FOXO3 candidacy, The Journals of Gerontology: Series A, 70, 110, 10.1093/gerona/glu166 · DOI
  10. Chandra, 2012, Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation, Molecular Cell, 47, 203, 10.1016/j.molcel.2012.06.010 · DOI · Paper page
  11. Chandra, 2015, Global reorganization of the nuclear landscape in senescent cells, Cell Reports, 10, 471, 10.1016/j.celrep.2014.12.055 · DOI · Paper page
  12. Choi, 2008, Age-related changes in Drosophila midgut are associated with PVF2, a PDGF/VEGF-like growth factor, Aging Cell, 7, 318, 10.1111/j.1474-9726.2008.00380.x · DOI
  13. Clausen, 2010, p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy, Autophagy, 6, 330, 10.4161/auto.6.3.11226 · DOI
  14. Di Malta, 2019, Transcriptional regulation of autophagy: mechanisms and diseases, Frontiers in Cell and Developmental Biology, 7, 10.3389/fcell.2019.00114 · DOI · Paper page
  15. Dodt, 2012, FLEXBAR-Flexible barcode and adapter processing for Next-Generation sequencing platforms, Biology, 1, 895, 10.3390/biology1030895 · DOI
  16. Ebert, 2004, Su(var) genes regulate the balance between euchromatin and heterochromatin in Drosophila, Genes & Development, 18, 2973, 10.1101/gad.323004 · DOI
  17. Fan, 2015, Rapamycin preserves gut homeostasis during Drosophila aging, Oncotarget, 6, 35274, 10.18632/oncotarget.5895 · DOI
  18. Filimonenko, 2010, The selective macroautophagic degradation of aggregated proteins requires the PI3P-Binding protein alfy, Molecular Cell, 38, 265, 10.1016/j.molcel.2010.04.007 · DOI
  19. Finlan, 2008, Recruitment to the nuclear periphery can alter expression of genes in human cells, PLOS Genetics, 4, 10.1371/journal.pgen.1000039 · DOI
  20. Finley, 2003, Blue cheese mutations define a novel, conserved gene involved in progressive neural degeneration, The Journal of Neuroscience, 23, 1254, 10.1523/JNEUROSCI.23-04-01254.2003 · DOI
  21. Füllgrabe, 2016, Transcriptional regulation of mammalian autophagy at a glance, Journal of Cell Science, 129, 3059, 10.1242/jcs.188920 · DOI
  22. Garelick, 2013, Chronic rapamycin treatment or lack of S6K1 does not reduce ribosome activity in vivo, Cell Cycle, 12, 2493, 10.4161/cc.25512 · DOI
  23. Gong, 2015, Histone modifications change with age, dietary restriction and rapamycin treatment in mouse brain, Oncotarget, 6, 15882, 10.18632/oncotarget.4137 · DOI
  24. Grewal, 2007, Heterochromatin revisited, Nature Reviews Genetics, 8, 35, 10.1038/nrg2008 · DOI · Paper page
  25. Guo, 2014, PGRP-SC2 promotes gut immune homeostasis to limit commensal dysbiosis and extend lifespan, Cell, 156, 109, 10.1016/j.cell.2013.12.018 · DOI
  26. Hansen, 2018, Autophagy as a promoter of longevity: insights from model organisms, Nature Reviews Molecular Cell Biology, 19, 579, 10.1038/s41580-018-0033-y · DOI · Paper page
  27. Harman, 1991, The aging process: major risk factor for disease and death, PNAS, 88, 5360, 10.1073/pnas.88.12.5360 · DOI
  28. Hauer, 2017, Chromatin and nucleosome dynamics in DNA damage and repair, Genes & Development, 31, 2204, 10.1101/gad.307702.117 · DOI
  29. Hu, 2014, Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging, Genes & Development, 28, 396, 10.1101/gad.233221.113 · DOI
  30. Ivanov, 2013, Lysosome-mediated processing of chromatin in senescence, Journal of Cell Biology, 202, 129, 10.1083/jcb.201212110 · DOI · Paper page
  31. Jiang, 2012, Intestinal stem cell function in Drosophila and mice, Current Opinion in Genetics & Development, 22, 354, 10.1016/j.gde.2012.04.002 · DOI
  32. Johnson, 2015, Genetic evidence for common pathways in human age-related diseases, Aging Cell, 14, 809, 10.1111/acel.12362 · DOI · Paper page
  33. Jung, 2010, mTOR regulation of autophagy, FEBS Letters, 584, 1287, 10.1016/j.febslet.2010.01.017 · DOI · Paper page
  34. Kapahi, 2004, Regulation of lifespan in Drosophila by modulation of genes in the TOR signaling pathway, Current Biology, 14, 885, 10.1016/j.cub.2004.03.059 · DOI · Paper page
  35. Kenyon, 2010, The genetics of ageing, Nature, 464, 504, 10.1038/nature08980 · DOI · Paper page
  36. Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nature Methods, 12, 357, 10.1038/nmeth.3317 · DOI · Paper page
  37. Kraft, 2012, Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy, The EMBO Journal, 31, 3691, 10.1038/emboj.2012.225 · DOI
  38. Kumsta, 2019, The autophagy receptor p62/SQST-1 promotes proteostasis and longevity in C. elegans by inducing autophagy, Nature Communications, 10, 10.1038/s41467-019-13540-4 · DOI
  39. Lapierre, 2015, Transcriptional and epigenetic regulation of autophagy in aging, Autophagy, 11, 867, 10.1080/15548627.2015.1034410 · DOI
  40. Larson, 2012, Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis, PLOS Genetics, 8, 10.1371/journal.pgen.1002473 · DOI · Paper page
  41. Lattanzi, 2014, Lamins are rapamycin targets that impact human longevity: a study in centenarians, Journal of Cell Science, 127, 147, 10.1242/jcs.133983 · DOI
  42. Lee, 2015, eIF3 targets cell-proliferation messenger RNAs for translational activation or repression, Nature, 522, 111, 10.1038/nature14267 · DOI
  43. Lee, 2016, eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation, Nature, 536, 96, 10.1038/nature18954 · DOI
  44. Lemaitre, 2013, The digestive tract of Drosophila Melanogaster, Annual Review of Genetics, 47, 377, 10.1146/annurev-genet-111212-133343 · DOI
  45. Li, 2009, The sequence alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 · DOI · Paper page
  46. Li, 2014, Rapamycin: one drug, many effects, Cell Metabolism, 19, 373, 10.1016/j.cmet.2014.01.001 · DOI · Paper page
  47. Luger, 2012, New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?, Nature Reviews Molecular Cell Biology, 13, 436, 10.1038/nrm3382 · DOI
  48. Martina, 2012, MTORC1 functions as a transcriptional regulator of autophagy by preventing nuclear transport of TFEB, Autophagy, 8, 903, 10.4161/auto.19653 · DOI · Paper page
  49. Martins, 2018, How to catch a smurf? - Ageing and beyond… In vivo Assessment of Intestinal Permeability in Multiple Model Organisms, Bio-Protocol, 8, 10.21769/BioProtoc.2722 · DOI
  50. Matilainen, 2017, The chromatin remodeling factor ISW-1 integrates organismal responses against nuclear and mitochondrial stress, Nature Communications, 8, 10.1038/s41467-017-01903-8 · DOI
  51. Memisoglu, 2019, PP2C phosphatases promote autophagy by dephosphorylation of the Atg1 complex, PNAS, 116, 1613, 10.1073/pnas.1817078116 · DOI
  52. Mizushima, 2010, Methods in mammalian autophagy research, Cell, 140, 313, 10.1016/j.cell.2010.01.028 · DOI · Paper page
  53. Nagy, 2015, How and why to study autophagy in Drosophila: it's more than just a garbage chute, Methods, 75, 151, 10.1016/j.ymeth.2014.11.016 · DOI · Paper page
  54. Nakatogawa, 2012, The autophagy-related protein kinase Atg1 interacts with the ubiquitin-like protein Atg8 via the Atg8 family interacting motif to facilitate autophagosome formation, Journal of Biological Chemistry, 287, 28503, 10.1074/jbc.C112.387514 · DOI
  55. Ni, 2012, Two SET domain containing genes link epigenetic changes and aging in Caenorhabditis elegans, Aging Cell, 11, 315, 10.1111/j.1474-9726.2011.00785.x · DOI
  56. Noda, 2015, Atg1 family kinases in autophagy initiation, Cellular and Molecular Life Sciences, 72, 3083, 10.1007/s00018-015-1917-z · DOI
  57. Oeste, 2013, Interactions between autophagic and endo-lysosomal markers in endothelial cells, Histochemistry and Cell Biology, 139, 659, 10.1007/s00418-012-1057-6 · DOI
  58. Pal, 2016, Epigenetics and aging, Science Advances, 2, 10.1126/sciadv.1600584 · DOI · Paper page
  59. Partridge, 2018, Facing up to the global challenges of ageing, Nature, 561, 45, 10.1038/s41586-018-0457-8 · DOI · Paper page
  60. Partridge, 2020, The quest to slow ageing through drug discovery, Nature Reviews Drug Discovery, 19, 513, 10.1038/s41573-020-0067-7 · DOI · Paper page
  61. Passtoors, 2013, Gene expression analysis of mTOR pathway: association with human longevity, Aging Cell, 12, 24, 10.1111/acel.12015 · DOI
  62. Pertea, 2015, StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nature Biotechnology, 33, 290, 10.1038/nbt.3122 · DOI
  63. Regan, 2016, Sex difference in pathology of the ageing gut mediates the greater response of female lifespan to dietary restriction, eLife, 5, 10.7554/eLife.10956 · DOI
  64. Regan, 2020, Dietary restriction and insulin‐like signalling pathways as adaptive plasticity: a synthesis and re‐evaluation, Functional Ecology, 34, 107, 10.1111/1365-2435.13418 · DOI
  65. Ren, 2009, Conditional inhibition of autophagy genes in adult Drosophila impairs immunity without compromising longevity, Experimental Gerontology, 44, 228, 10.1016/j.exger.2008.10.002 · DOI
  66. Rera, 2012, Intestinal barrier dysfunction links metabolic and inflammatory markers of aging to death in Drosophila, PNAS, 109, 21528, 10.1073/pnas.1215849110 · DOI
  67. Resnik-Docampo, 2017, Tricellular junctions regulate intestinal stem cell behaviour to maintain homeostasis, Nature Cell Biology, 19, 52, 10.1038/ncb3454 · DOI
  68. Salazar, 2018, Intestinal snakeskin limits microbial dysbiosis during aging and promotes longevity, iScience, 9, 229, 10.1016/j.isci.2018.10.022 · DOI
  69. Sancho, 2015, Stem cell and progenitor fate in the mammalian intestine: notch and lateral inhibition in homeostasis and disease, EMBO Reports, 16, 571, 10.15252/embr.201540188 · DOI
  70. Scott, 2004, Role and regulation of starvation-induced autophagy in the Drosophila fat body, Developmental Cell, 7, 167, 10.1016/j.devcel.2004.07.009 · DOI
  71. Sim, 2019, The BEACH domain is critical for blue cheese function in a spatial and epistatic autophagy hierarchy, Frontiers in Cell and Developmental Biology, 7, 10.3389/fcell.2019.00129 · DOI
  72. Singh, 2010, Excess histone levels mediate cytotoxicity via multiple mechanisms, Cell Cycle, 9, 4236, 10.4161/cc.9.20.13636 · DOI
  73. Tain, 2017, A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance, Molecular Systems Biology, 13, 10.15252/msb.20177663 · DOI
  74. Ulgherait, 2014, AMPK modulates tissue and organismal aging in a non-cell-autonomous manner, Cell Reports, 8, 1767, 10.1016/j.celrep.2014.08.006 · DOI
  75. Unnikrishnan, 2020, Is rapamycin a dietary restriction mimetic?, The Journals of Gerontology: Series A, 75, 4, 10.1093/gerona/glz060 · DOI
  76. Wang, 2017, Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment, Genome Biology, 18, 10.1186/s13059-017-1186-2 · DOI
  77. Wei, 2015, Epigenetic regulation of autophagy by the methyltransferase EZH2 through an MTOR-dependent pathway, Autophagy, 11, 2309, 10.1080/15548627.2015.1117734 · DOI
  78. Yeh, 2010, Autophosphorylation within the Atg1 activation loop is required for both kinase activity and the induction of autophagy in Saccharomyces cerevisiae, Genetics, 185, 871, 10.1534/genetics.110.116566 · DOI · Paper page
  79. Zaffagnini, 2016, Mechanisms of selective autophagy, Journal of Molecular Biology, 428, 1714, 10.1016/j.jmb.2016.02.004 · DOI

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Metadata

Authors
Lu, Y.-X., Regan, J. C., Eßer, J., Drews, L. F., Weinseis, T., Stinn, J., Hahn, O., Miller, R. A., Grönke, S., & Partridge, L.
Affiliations
  • Max Planck Institute for Biology of Ageing, Cologne, Germany
  • Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
  • Department of Pathology, University of Michigan, Ann Arbor, United States
Venue
eLife
Published
2021-05-14
Volume
10
ISSN
2050-084X
Cited by
76
References
19
Language
en
Funders
  • Horizon 2020 Framework Programme (741989)
  • European Molecular Biology Organization (ALTF419-2014)
  • Glenn Foundation for Medical Research
  • Max Planck Institute for Biology of Ageing (Open-access funding)

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