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González JT, Thrush K, Meer M, Levine ME, Higgins-Chen AT. Age-Invariant Genes: Multi-Tissue Identification and Characterization of Murine Reference Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588721. [PMID: 38645168 PMCID: PMC11030416 DOI: 10.1101/2024.04.09.588721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Studies of the aging transcriptome focus on genes that change with age. But what can we learn from age-invariant genes-those that remain unchanged throughout the aging process? These genes also have a practical application: they serve as reference genes (often called housekeeping genes) in expression studies. Reference genes have mostly been identified and validated in young organisms, and no systematic investigation has been done across the lifespan. Here, we build upon a common pipeline for identifying reference genes in RNA-seq datasets to identify age-invariant genes across seventeen C57BL/6 mouse tissues (brain, lung, bone marrow, muscle, white blood cells, heart, small intestine, kidney, liver, pancreas, skin, brown, gonadal, marrow, and subcutaneous adipose tissue) spanning 1 to 21+ months of age. We identify 9 pan-tissue age-invariant genes and many tissue-specific age-invariant genes. These genes are stable across the lifespan and are validated in independent bulk RNA-seq datasets and RT-qPCR. We find age-invariant genes have shorter transcripts on average and are enriched for CpG islands. Interestingly, pathway enrichment analysis for age-invariant genes identifies an overrepresentation of molecular functions associated with some, but not all, hallmarks of aging. Thus, though hallmarks of aging typically involve changes in cell maintenance mechanisms, select genes associated with these hallmarks resist fluctuations in expression with age. Finally, our analysis concludes no classical reference gene is appropriate for aging studies in all tissues. Instead, we provide tissue-specific and pan-tissue genes for assays utilizing reference gene normalization (i.e., RT-qPCR) that can be applied to animals across the lifespan.
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Affiliation(s)
- John T. González
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Kyra Thrush
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Margarita Meer
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Morgan E. Levine
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Altos Labs, San Diego Institute of Sciences, San Diego, CA, USA
| | - Albert T. Higgins-Chen
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven CT, USA
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Lu YR, Tian X, Sinclair DA. The Information Theory of Aging. NATURE AGING 2023; 3:1486-1499. [PMID: 38102202 DOI: 10.1038/s43587-023-00527-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/02/2023] [Indexed: 12/17/2023]
Abstract
Information storage and retrieval is essential for all life. In biology, information is primarily stored in two distinct ways: the genome, comprising nucleic acids, acts as a foundational blueprint and the epigenome, consisting of chemical modifications to DNA and histone proteins, regulates gene expression patterns and endows cells with specific identities and functions. Unlike the stable, digital nature of genetic information, epigenetic information is stored in a digital-analog format, susceptible to alterations induced by diverse environmental signals and cellular damage. The Information Theory of Aging (ITOA) states that the aging process is driven by the progressive loss of youthful epigenetic information, the retrieval of which via epigenetic reprogramming can improve the function of damaged and aged tissues by catalyzing age reversal.
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Affiliation(s)
- Yuancheng Ryan Lu
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David A Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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Harvanek ZM, Boks MP, Vinkers CH, Higgins-Chen AT. The Cutting Edge of Epigenetic Clocks: In Search of Mechanisms Linking Aging and Mental Health. Biol Psychiatry 2023; 94:694-705. [PMID: 36764569 PMCID: PMC10409884 DOI: 10.1016/j.biopsych.2023.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Individuals with psychiatric disorders are at increased risk of age-related diseases and early mortality. Recent studies demonstrate that this link between mental health and aging is reflected in epigenetic clocks, aging biomarkers based on DNA methylation. The reported relationships between epigenetic clocks and mental health are mostly correlational, and the mechanisms are poorly understood. Here, we review recent progress concerning the molecular and cellular processes underlying epigenetic clocks as well as novel technologies enabling further studies of the causes and consequences of epigenetic aging. We then review the current literature on how epigenetic clocks relate to specific aspects of mental health, such as stress, medications, substance use, health behaviors, and symptom clusters. We propose an integrated framework where mental health and epigenetic aging are each broken down into multiple distinct processes, which are then linked to each other, using stress and schizophrenia as examples. This framework incorporates the heterogeneity and complexity of both mental health conditions and aging, may help reconcile conflicting results, and provides a basis for further hypothesis-driven research in humans and model systems to investigate potentially causal mechanisms linking aging and mental health.
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Affiliation(s)
- Zachary M Harvanek
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Marco P Boks
- Department of Psychiatry, University Medical Center Utrecht Brain Center, University of Utrecht, Utrecht, the Netherlands
| | - Christiaan H Vinkers
- Department of Psychiatry, Amsterdam University Medical Center, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Mood, Anxiety, Psychosis, Sleep & Stress program, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Albert T Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut; Department of Pathology, Yale University School of Medicine, New Haven, Connecticut.
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En A, Watanabe K, Ayusawa D, Fujii M. The key role of a basic domain of histone H2B N-terminal tail in the action of 5-bromodeoxyuridine to induce cellular senescence. FEBS J 2023; 290:692-711. [PMID: 35882390 DOI: 10.1111/febs.16584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 06/28/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023]
Abstract
5-Bromodeoxyuridine (BrdU), a thymidine analogue, is an interesting reagent that modulates various biological phenomena. BrdU, upon incorporation into DNA, causes destabilized nucleosome positioning which leads to changes in heterochromatin organization and gene expression in cells. We have previously shown that BrdU effectively induces cellular senescence, a phenomenon of irreversible growth arrest in mammalian cells. Identification of the mechanism of action of BrdU would provide a novel insight into the molecular mechanisms of cellular senescence. Here, we showed that a basic domain in the histone H2B N-terminal tail, termed the HBR (histone H2B repression) domain, is involved in the action of BrdU. Notably, deletion of the HBR domain causes destabilized nucleosome positioning and derepression of gene expression, as does BrdU. We also showed that the genes up-regulated by BrdU significantly overlapped with those by deletion of the HBR domain, the result of which suggested that BrdU and deletion of the HBR domain act in a similar way. Furthermore, we showed that decreased HBR domain function induced cellular senescence or facilitated the induction of cellular senescence. These findings indicated that the HBR domain is crucially involved in the action of BrdU, and also suggested that disordered nucleosome organization may be involved in the induction of cellular senescence.
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Affiliation(s)
- Atsuki En
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Kazuaki Watanabe
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Dai Ayusawa
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Michihiko Fujii
- Graduate School of Nanobioscience, Yokohama City University, Japan
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Abstract
Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' physiological functioning. However, achieving this aim requires measures of biological age and rates of ageing at the molecular level. Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build 'ageing clocks' with demonstrated capacity to identify new biomarkers of biological ageing.
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Affiliation(s)
- Jarod Rutledge
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamilton Oh
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
- Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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Xue Y, Wang J, He Y, Patra P, Gao YQ. Multi-scale gene regulation mechanism: Spatiotemporal transmission of genetic information. Curr Opin Struct Biol 2022; 77:102487. [PMID: 36274420 DOI: 10.1016/j.sbi.2022.102487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/09/2022] [Accepted: 09/18/2022] [Indexed: 12/14/2022]
Abstract
Gene expression is regulated by many factors, including transcription factors, chromatin three-dimensional topology, modifications of DNA and histone proteins, and non-coding RNAs. The execution of these complex mechanisms requires an effectively coordinated regulation system. In this review, we emphasize that the multi-scale heterogeneous DNA sequence plays a fundamental and important role for gene expression activity and usage of different means of epigenetic regulation. We illustrate here that the chromatin structure organization provides a stage for spatiotemporal regulation between different genes or gene modules and to realize their downstream functional cooperation. Such a perspective expands our understanding of the central dogma: In addition to one-dimensional sequence information, inter-gene interactions can also be transferred from DNA and RNA to protein levels.
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Affiliation(s)
- Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingyao Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
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