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Yheskel M, Hatch HM, Pedrosa E, Terry BK, Siebels A, Zheng X, Blok LR, Fencková M, Sidoli S, Schenck A, Zheng D, Lachman H, Secombe J. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Res 2024; 52:6201-6219. [PMID: 38597673 PMCID: PMC11194071 DOI: 10.1093/nar/gkae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024] Open
Abstract
Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bethany K Terry
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aubrey A Siebels
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiang Yu Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura E R Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Michaela Fencková
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Ceske Budejovice 370 05, Czechia
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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2
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Rogers MF, Marshall OJ, Secombe J. KDM5-mediated activation of genes required for mitochondrial biology is necessary for viability in Drosophila. Development 2023; 150:dev202024. [PMID: 37800333 PMCID: PMC10651110 DOI: 10.1242/dev.202024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Histone-modifying proteins play important roles in the precise regulation of the transcriptional programs that coordinate development. KDM5 family proteins interact with chromatin through demethylation of H3K4me3 as well as demethylase-independent mechanisms that remain less understood. To gain fundamental insights into the transcriptional activities of KDM5 proteins, we examined the essential roles of the single Drosophila Kdm5 ortholog during development. KDM5 performs crucial functions in the larval neuroendocrine prothoracic gland, providing a model to study its role in regulating key gene expression programs. Integrating genome binding and transcriptomic data, we identify that KDM5 regulates the expression of genes required for the function and maintenance of mitochondria, and we find that loss of KDM5 causes morphological changes to mitochondria. This is key to the developmental functions of KDM5, as expression of the mitochondrial biogenesis transcription factor Ets97D, homolog of GABPα, is able to suppress the altered mitochondrial morphology as well as the lethality of Kdm5 null animals. Together, these data establish KDM5-mediated cellular functions that are important for normal development and could contribute to KDM5-linked disorders when dysregulated.
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Affiliation(s)
- Michael F. Rogers
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Owen J. Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart TAS 7000, Australia
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Statsenko Y, Kuznetsov NV, Morozova D, Liaonchyk K, Simiyu GL, Smetanina D, Kashapov A, Meribout S, Gorkom KNV, Hamoudi R, Ismail F, Ansari SA, Emerald BS, Ljubisavljevic M. Reappraisal of the Concept of Accelerated Aging in Neurodegeneration and Beyond. Cells 2023; 12:2451. [PMID: 37887295 PMCID: PMC10605227 DOI: 10.3390/cells12202451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Genetic and epigenetic changes, oxidative stress and inflammation influence the rate of aging, which diseases, lifestyle and environmental factors can further accelerate. In accelerated aging (AA), the biological age exceeds the chronological age. OBJECTIVE The objective of this study is to reappraise the AA concept critically, considering its weaknesses and limitations. METHODS We reviewed more than 300 recent articles dealing with the physiology of brain aging and neurodegeneration pathophysiology. RESULTS (1) Application of the AA concept to individual organs outside the brain is challenging as organs of different systems age at different rates. (2) There is a need to consider the deceleration of aging due to the potential use of the individual structure-functional reserves. The latter can be restored by pharmacological and/or cognitive therapy, environment, etc. (3) The AA concept lacks both standardised terminology and methodology. (4) Changes in specific molecular biomarkers (MBM) reflect aging-related processes; however, numerous MBM candidates should be validated to consolidate the AA theory. (5) The exact nature of many potential causal factors, biological outcomes and interactions between the former and the latter remain largely unclear. CONCLUSIONS Although AA is commonly recognised as a perspective theory, it still suffers from a number of gaps and limitations that assume the necessity for an updated AA concept.
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Affiliation(s)
- Yauhen Statsenko
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Big Data Analytic Center, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Nik V. Kuznetsov
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Daria Morozova
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Katsiaryna Liaonchyk
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Gillian Lylian Simiyu
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Darya Smetanina
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Aidar Kashapov
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Sarah Meribout
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Klaus Neidl-Van Gorkom
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Rifat Hamoudi
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London NW3 2PS, UK
| | - Fatima Ismail
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Suraiya Anjum Ansari
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Bright Starling Emerald
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Milos Ljubisavljevic
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Zraly CB, Schultz R, Diaz MO, Dingwall AK. New twists of a TAIL: novel insights into the histone binding properties of a highly conserved PHD finger cluster within the MLR family of H3K4 mono-methyltransferases. Nucleic Acids Res 2023; 51:9672-9689. [PMID: 37638761 PMCID: PMC10570056 DOI: 10.1093/nar/gkad698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
Enhancer activation by the MLR family of H3K4 mono-methyltransferases requires proper recognition of histones for the deposition of the mono-methyl mark. MLR proteins contain two clusters of PHD zinc finger domains implicated in chromatin regulation. The second cluster is the most highly conserved, preserved as an ancient three finger functional unit throughout evolution. Studies of the isolated 3rd PHD finger within this cluster suggested specificity for the H4 [aa16-20] tail region. We determined the histone binding properties of the full three PHD finger cluster b module (PHDb) from the Drosophila Cmi protein which revealed unexpected recognition of an extended region of H3. Importantly, the zinc finger spacer separating the first two PHDb fingers from the third is critical for proper alignment and coordination among fingers for maximal histone engagement. Human homologs, MLL3 and MLL4, also show conservation of H3 binding, expanding current views of histone recognition for this class of proteins. We further implicate chromatin remodeling by the SWI/SNF complex as a possible mechanism for the accessibility of PHDb to globular regions of histone H3 beyond the tail region. Our results suggest a two-tail histone recognition mechanism by the conserved PHDb domain involving a flexible hinge to promote interdomain coordination.
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Affiliation(s)
- Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Richard Schultz
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Manuel O Diaz
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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5
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Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci 2023; 10:1270285. [PMID: 37877123 PMCID: PMC10591336 DOI: 10.3389/fmolb.2023.1270285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Aging affects nearly all aspects of our cells, from our DNA to our proteins to how our cells handle stress and communicate with each other. Age-related chromatin changes are of particular interest because chromatin can dynamically respond to the cellular and organismal environment, and many modifications at chromatin are reversible. Changes at chromatin occur during aging, and evidence from model organisms suggests that chromatin factors could play a role in modulating the aging process itself, as altering proteins that work at chromatin often affect the lifespan of yeast, worms, flies, and mice. The field of chromatin and aging is rapidly expanding, and high-resolution genomics tools make it possible to survey the chromatin environment or track chromatin factors implicated in longevity with precision that was not previously possible. In this review, we discuss the state of chromatin and aging research. We include examples from yeast, Drosophila, mice, and humans, but we particularly focus on the commonly used aging model, the worm Caenorhabditis elegans, in which there are many examples of chromatin factors that modulate longevity. We include evidence of both age-related changes to chromatin and evidence of specific chromatin factors linked to longevity in core histones, nuclear architecture, chromatin remodeling, and histone modifications.
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Affiliation(s)
| | - Siu Sylvia Lee
- Lee Lab, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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6
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DiVito Evans A, Fairbanks RA, Schmidt P, Levine MT. Histone methylation regulates reproductive diapause in Drosophila melanogaster. PLoS Genet 2023; 19:e1010906. [PMID: 37703303 PMCID: PMC10499233 DOI: 10.1371/journal.pgen.1010906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Fluctuating environments threaten fertility and viability. To better match the immediate, local environment, many organisms adopt alternative phenotypic states, a phenomenon called "phenotypic plasticity." Natural populations that predictably encounter fluctuating environments tend to be more plastic than conspecific populations that encounter a constant environment, suggesting that phenotypic plasticity can be adaptive. Despite pervasive evidence of such "adaptive phenotypic plasticity," gene regulatory mechanisms underlying plasticity remains poorly understood. Here we test the hypothesis that environment-dependent phenotypic plasticity is mediated by epigenetic factors. To test this hypothesis, we exploit the adaptive reproductive arrest of Drosophila melanogaster females, called diapause. Using an inbred line from a natural population with high diapause plasticity, we demonstrate that diapause is determined epigenetically: only a subset of genetically identical individuals enter diapause and this diapause plasticity is epigenetically transmitted for at least three generations. Upon screening a suite of epigenetic marks, we discovered that the active histone marks H3K4me3 and H3K36me1 are depleted in diapausing ovaries. Using ovary-specific knockdown of histone mark writers and erasers, we demonstrate that H3K4me3 and H3K36me1 depletion promotes diapause. Given that diapause is highly polygenic, that is, distinct suites of alleles mediate diapause plasticity across distinct genotypes, we also investigated the potential for genetic variation in diapause-determining epigenetic marks. Specifically, we asked if these histone marks were similarly depleted in diapause of a genotypically distinct line. We found evidence of divergence in both the gene expression program and histone mark abundance. This study reveals chromatin determinants of phenotypic plasticity and suggests that these determinants may be genotype-dependent, offering new insight into how organisms may exploit and evolve epigenetic mechanisms to persist in fluctuating environments.
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Affiliation(s)
- Abigail DiVito Evans
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Regina A. Fairbanks
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Paul Schmidt
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mia T. Levine
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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7
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Mocciaro E, Giambruno R, Micheloni S, Cernilogar FM, Andolfo A, Consonni C, Pannese M, Ferri G, Runfola V, Schotta G, Gabellini D. WDR5 is required for DUX4 expression and its pathological effects in FSHD muscular dystrophy. Nucleic Acids Res 2023; 51:5144-5161. [PMID: 37021550 PMCID: PMC10250208 DOI: 10.1093/nar/gkad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most prevalent neuromuscular disorders. The disease is linked to copy number reduction and/or epigenetic alterations of the D4Z4 macrosatellite on chromosome 4q35 and associated with aberrant gain of expression of the transcription factor DUX4, which triggers a pro-apoptotic transcriptional program leading to muscle wasting. As today, no cure or therapeutic option is available to FSHD patients. Given its centrality in FSHD, blocking DUX4 expression with small molecule drugs is an attractive option. We previously showed that the long non protein-coding RNA DBE-T is required for aberrant DUX4 expression in FSHD. Using affinity purification followed by proteomics, here we identified the chromatin remodeling protein WDR5 as a novel DBE-T interactor and a key player required for the biological activity of the lncRNA. We found that WDR5 is required for the expression of DUX4 and its targets in primary FSHD muscle cells. Moreover, targeting WDR5 rescues both cell viability and myogenic differentiation of FSHD patient cells. Notably, comparable results were obtained by pharmacological inhibition of WDR5. Importantly, WDR5 targeting was safe to healthy donor muscle cells. Our results support a pivotal role of WDR5 in the activation of DUX4 expression identifying a druggable target for an innovative therapeutic approach for FSHD.
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Affiliation(s)
- Emanuele Mocciaro
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Roberto Giambruno
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano Micheloni
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Annapaola Andolfo
- ProMeFa, Proteomics and Metabolomics Facility, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Cristina Consonni
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Maria Pannese
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Giulia Ferri
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Valeria Runfola
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
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la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
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Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
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9
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González-Rodríguez P, Füllgrabe J, Joseph B. The hunger strikes back: an epigenetic memory for autophagy. Cell Death Differ 2023:10.1038/s41418-023-01159-4. [PMID: 37031275 DOI: 10.1038/s41418-023-01159-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Historical and demographical human cohorts of populations exposed to famine, as well as animal studies, revealed that exposure to food deprivation is associated to lasting health-related effects for the exposed individuals, as well as transgenerational effects in their offspring that affect their diseases' risk and overall longevity. Autophagy, an evolutionary conserved catabolic process, serves as cellular response to cope with nutrient starvation, allowing the mobilization of an internal source of stored nutrients and the production of energy. We review the evidence obtained in multiple model organisms that support the idea that autophagy induction, including through dietary regimes based on reduced food intake, is in fact associated to improved health span and extended lifespan. Thereafter, we expose autophagy-induced chromatin remodeling, such as DNA methylation and histone posttranslational modifications that are known heritable epigenetic marks, as a plausible mechanism for transgenerational epigenetic inheritance of hunger.
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Affiliation(s)
- Patricia González-Rodríguez
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Füllgrabe
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Bertrand Joseph
- Institute of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Stockholm, Sweden.
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10
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Yheskel M, Sidoli S, Secombe J. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. Epigenetics Chromatin 2023; 16:8. [PMID: 36803422 PMCID: PMC9938590 DOI: 10.1186/s13072-023-00481-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription regulation, we used TurboID proximity labeling to identify KDM5-interacting proteins. RESULTS Using Drosophila melanogaster, we enriched for biotinylated proteins from KDM5-TurboID-expressing adult heads using a newly generated control for DNA-adjacent background in the form of dCas9:TurboID. Mass spectrometry analyses of biotinylated proteins identified both known and novel candidate KDM5 interactors, including members of the SWI/SNF and NURF chromatin remodeling complexes, the NSL complex, Mediator, and several insulator proteins. CONCLUSIONS Combined, our data shed new light on potential demethylase-independent activities of KDM5. In the context of KDM5 dysregulation, these interactions may play key roles in the alteration of evolutionarily conserved transcriptional programs implicated in human disorders.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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11
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Ugur FS, Kelly MJS, Fujimori DG. Chromatin Sensing by the Auxiliary Domains of KDM5C Regulates Its Demethylase Activity and Is Disrupted by X-linked Intellectual Disability Mutations. J Mol Biol 2023; 435:167913. [PMID: 36495919 PMCID: PMC10247153 DOI: 10.1016/j.jmb.2022.167913] [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] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/10/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The H3K4me3 chromatin modification, a hallmark of promoters of actively transcribed genes, is dynamically removed by the KDM5 family of histone demethylases. The KDM5 demethylases have a number of accessory domains, two of which, ARID and PHD1, lie between the segments of the catalytic domain. KDM5C, which has a unique role in neural development, harbors a number of mutations adjacent to its accessory domains that cause X-linked intellectual disability (XLID). The roles of these accessory domains remain unknown, limiting an understanding of how XLID mutations affect KDM5C activity. Through in vitro binding and kinetic studies using nucleosomes, we find that while the ARID domain is required for efficient nucleosome demethylation, the PHD1 domain alone has an inhibitory role in KDM5C catalysis. In addition, the unstructured linker region between the ARID and PHD1 domains interacts with PHD1 and is necessary for nucleosome binding. Our data suggests a model in which the PHD1 domain inhibits DNA recognition by KDM5C. This inhibitory effect is relieved by the H3 tail, enabling recognition of flanking DNA on the nucleosome. Importantly, we find that XLID mutations adjacent to the ARID and PHD1 domains break this regulation by enhancing DNA binding, resulting in the loss of specificity of substrate chromatin recognition and rendering demethylase activity lower in the presence of flanking DNA. Our findings suggest a model by which specific XLID mutations could alter chromatin recognition and enable euchromatin-specific dysregulation of demethylation by KDM5C.
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Affiliation(s)
- Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, 600 16th St., San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, 600 16th St., San Francisco, CA 94158, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, 600 16th St., San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, 600 16th St., San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, 600 16th St., San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, 600 16th St., San Francisco, CA 94158, USA.
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12
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Zhang SM, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:113-137. [PMID: 37751138 DOI: 10.1007/978-3-031-38176-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.
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Affiliation(s)
- Shang-Min Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
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13
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Zhang Q, Kong WL, Yuan JJ, Chen Q, Gong CX, Liu L, Wang FX, Huang JC, Yang GQ, Zhou K, Xu R, Xiong XY, Yang QW. Redistribution of Histone Marks on Inflammatory Genes Associated With Intracerebral Hemorrhage-Induced Acute Brain Injury in Aging Rats. Front Neurosci 2022; 16:639656. [PMID: 35495024 PMCID: PMC9051396 DOI: 10.3389/fnins.2022.639656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The contribution of histone mark redistribution to the age-induced decline of endogenous neuroprotection remains unclear. In this study, we used an intracerebral hemorrhage (ICH)-induced acute brain injury rat model to study the transcriptional and chromatin responses in 13- and 22-month-old rats. Transcriptome analysis (RNA-seq) revealed that the expression of neuroinflammation-associated genes was systematically upregulated in ICH rat brains, irrespective of age. Further, we found that interferon-γ (IFN-γ) response genes were activated in both 13- and 22-month-old rats. Anti-IFN-γ treatment markedly reduced ICH-induced acute brain injury in 22-month-old rats. At the chromatin level, ICH induced the redistribution of histone modifications in the promoter regions, especially H3K4me3 and H3K27me3, in neuroinflammation-associated genes in 13- and 22-month-old rats, respectively. Moreover, ICH-induced histone mark redistribution and gene expression were found to be correlated. Collectively, these findings demonstrate that histone modifications related to gene expression are extensively regulated in 13- and 22-month-old rats and that anti-IFN-γ is effective for ICH treatment, highlighting the potential of developing therapies targeting histone modifications to cure age-related diseases, including brain injury and neuroinflammation.
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Affiliation(s)
- Qin Zhang
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Wei-lin Kong
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Jun-Jie Yuan
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Qiong Chen
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Chang-Xiong Gong
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Liang Liu
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Fa-Xiang Wang
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Jia-Cheng Huang
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Guo-Qiang Yang
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Kai Zhou
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Rui Xu
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
| | - Xiao-Yi Xiong
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
- Acupuncture and Tuina School, Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Chronobiology Key Laboratory of Sichuan, Chengdu, China
- Xiao-Yi Xiong ;
| | - Qing-Wu Yang
- Department of Neurology, Xinqiao Hospital, The Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Qing-Wu Yang
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14
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Xiao Y, Liu F, Kong Q, Zhu X, Wang H, Li S, Jiang N, Yu C, Yun L. Metformin induces S-adenosylmethionine restriction to extend the Caenorhabditis elegans healthspan through H3K4me3 modifiers. Aging Cell 2022; 21:e13567. [PMID: 35146893 PMCID: PMC8920454 DOI: 10.1111/acel.13567] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 01/14/2023] Open
Abstract
Metformin, a widely prescribed first‐line drug for the treatment of type II diabetes mellitus, has been shown to extend lifespan and delay the onset of age‐related diseases. The precisely mechanisms by which these effects are realized remain elusive. We find that metformin exposure is restricted to adults, which is sufficient to extend lifespan. However, limiting metformin exposure to the larvae has no significant effect on Caenorhabditis elegans longevity. Here, we show that after metformin treatment, the level of S‐adenosylmethionine (SAM) is reduced in adults but not in the larvae. Potential mechanisms by which reduced SAM might increase lifespan include altering the histone methylation. However, the molecular connections between metformin, SAM limitation, methyltransferases, and healthspan‐associated phenotypes are unclear. Through genetic screening of C. elegans, we find that metformin promotes the healthspan through an H3K4 methyltransferase/demethylase complex to downregulate the targets, including mTOR and S6 kinase. Thus, our studies provide molecular links between meformin, SAM limitation, histone methylation, and healthspan and elucidate the mode action of metformin‐regulated healthspan extension will boost its therapeutic application in the treatment of human aging and age‐related diseases.
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Affiliation(s)
- Yi Xiao
- Institute of life sciences Zunyi Medical University Zunyi China
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
- College of Basic Medicine Zunyi Medical University Zunyi China
| | - Fang Liu
- College of Basic Medicine Zunyi Medical University Zunyi China
| | - Qinghong Kong
- Institute of life sciences Zunyi Medical University Zunyi China
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
| | - Xinting Zhu
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
- College of Basic Medicine Zunyi Medical University Zunyi China
| | - Haijuan Wang
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
- College of Basic Medicine Zunyi Medical University Zunyi China
| | - Sanhua Li
- Institute of life sciences Zunyi Medical University Zunyi China
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
| | - Nian Jiang
- Institute of life sciences Zunyi Medical University Zunyi China
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
| | - Changyan Yu
- Institute of life sciences Zunyi Medical University Zunyi China
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
| | - Liu Yun
- Institute of life sciences Zunyi Medical University Zunyi China
- Guizhou Provincial College‐based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines Zunyi Medical University Zunyi China
- College of Basic Medicine Zunyi Medical University Zunyi China
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15
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Caron M, Gely L, Garvis S, Adrait A, Couté Y, Palladino F, Fabrizio P. Loss of SET1/COMPASS methyltransferase activity reduces lifespan and fertility in Caenorhabditis elegans. Life Sci Alliance 2021; 5:5/3/e202101140. [PMID: 34893559 PMCID: PMC8675910 DOI: 10.26508/lsa.202101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/06/2023] Open
Abstract
Changes in histone post-translational modifications are associated with aging through poorly defined mechanisms. Histone 3 lysine 4 (H3K4) methylation at promoters is deposited by SET1 family methyltransferases acting within conserved multiprotein complexes known as COMPASS. Previous work yielded conflicting results about the requirement for H3K4 methylation during aging. Here, we reassessed the role of SET1/COMPASS-dependent H3K4 methylation in Caenorhabditis elegans lifespan and fertility by generating set-2(syb2085) mutant animals that express a catalytically inactive form of SET-2, the C. elegans SET1 homolog. We show that set-2(syb2085) animals retain the ability to form COMPASS, but have a marked global loss of H3K4 di- and trimethylation (H3K4me2/3). Reduced H3K4 methylation was accompanied by loss of fertility, as expected; however, in contrast to earlier studies, set-2(syb2085) mutants displayed a significantly shortened, not extended, lifespan and had normal intestinal fat stores. Other commonly used set-2 mutants were also short-lived, as was a cfp-1 mutant that lacks the SET1/COMPASS chromatin-targeting component. These results challenge previously held views and establish that WT H3K4me2/3 levels are essential for normal lifespan in C. elegans.
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Affiliation(s)
- Matthieu Caron
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Loïc Gely
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Steven Garvis
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Annie Adrait
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Yohann Couté
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Francesca Palladino
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Paola Fabrizio
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
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16
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Oleson BJ, Bazopoulou D, Jakob U. Shaping longevity early in life: developmental ROS and H3K4me3 set the clock. Cell Cycle 2021; 20:2337-2347. [PMID: 34657571 PMCID: PMC8794500 DOI: 10.1080/15384101.2021.1986317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Studies in Caenorhabditis elegans have revealed that even a genetically identical population of animals exposed to the same environment displays a remarkable level of variability in individual lifespan. Stochasticity factors, occurring seemingly by chance or at random, are thought to account for a large part of this variability. Recent studies in our lab using C. elegans now revealed that naturally occurring variations in the levels of reactive oxygen species experienced early in life contribute to the observed lifespan variability, and likely serve as stochasticity factors in aging. Here, we will highlight how developmental events can positively shape lifespan and stress responses via a redox-sensitive epigenetic regulator, and discuss the outstanding questions and future directions on the complex relationship between reactive oxygen species and aging.
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Affiliation(s)
- Bryndon J. Oleson
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Daphne Bazopoulou
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, USA,CONTACT Ursula Jakob Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, USA
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17
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Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
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18
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Punnia-Moorthy G, Hersey P, Emran AA, Tiffen J. Lysine Demethylases: Promising Drug Targets in Melanoma and Other Cancers. Front Genet 2021; 12:680633. [PMID: 34220955 PMCID: PMC8242339 DOI: 10.3389/fgene.2021.680633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic dysregulation has been implicated in a variety of pathological processes including carcinogenesis. A major group of enzymes that influence epigenetic modifications are lysine demethylases (KDMs) also known as "erasers" which remove methyl groups on lysine (K) amino acids of histones. Numerous studies have implicated aberrant lysine demethylase activity in a variety of cancers, including melanoma. This review will focus on the structure, classification and functions of KDMs in normal biology and the current knowledge of how KDMs are deregulated in cancer pathogenesis, emphasizing our interest in melanoma. We highlight the current knowledge gaps of KDMs in melanoma pathobiology and describe opportunities to increases our understanding of their importance in this disease. We summarize the progress of several pre-clinical compounds that inhibit KDMs and represent promising candidates for further investigation in oncology.
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Affiliation(s)
- Gaya Punnia-Moorthy
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Peter Hersey
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Abdullah Al Emran
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Jessamy Tiffen
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
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19
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Shen H, Zhang W, Huang Y, He Y, Hu G, Wang L, Peng B, Yi J, Li T, Rong R, Chen X, Liu J, Li W, Ohgi K, Li S, Rosenfeld MG, Liu W. The Dual Function of KDM5C in Both Gene Transcriptional Activation and Repression Promotes Breast Cancer Cell Growth and Tumorigenesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004635. [PMID: 33977073 PMCID: PMC8097366 DOI: 10.1002/advs.202004635] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/25/2020] [Indexed: 06/01/2023]
Abstract
Emerging evidence suggested that epigenetic regulators can exhibit both activator and repressor activities in gene transcriptional regulation and disease development, such as cancer. However, how these dual activities are regulated and coordinated in specific cellular contexts remains elusive. Here, it is reported that KDM5C, a repressive histone demethylase, unexpectedly activates estrogen receptor alpha (ERα)-target genes, and meanwhile suppresses type I interferons (IFNs) and IFN-stimulated genes (ISGs) to promote ERα-positive breast cancer cell growth and tumorigenesis. KDM5C-interacting protein, ZMYND8, is found to be involved in both processes. Mechanistically, KDM5C binds to active enhancers and recruits the P-TEFb complex to activate ERα-target genes, while inhibits TBK1 phosphorylation in the cytosol to repress type I IFNs and ISGs. Pharmacological inhibition of both ERα and KDM5C is effective in inhibiting cell growth and tumorigenesis. Taken together, it is revealed that the dual activator and repressor nature of an epigenetic regulator together contributes to cancer development.
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Affiliation(s)
- Hai‐feng Shen
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Wen‐juan Zhang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Ying Huang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Yao‐hui He
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Guo‐sheng Hu
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Lei Wang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Bing‐ling Peng
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Jia Yi
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Ting‐ting Li
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Rui Rong
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Xiao‐yan Chen
- School of Life SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Jun‐yi Liu
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Wen‐juan Li
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Kenny Ohgi
- Howard Hughes Medical InstituteDepartment of MedicineUniversity of California9500 Gilman Drive La JollaSan DiegoCA92093USA
| | - Shao‐Wei Li
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Michael G. Rosenfeld
- Howard Hughes Medical InstituteDepartment of MedicineUniversity of California9500 Gilman Drive La JollaSan DiegoCA92093USA
| | - Wen Liu
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
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20
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Belalcazar HM, Hendricks EL, Zamurrad S, Liebl FLW, Secombe J. The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction. Cell Rep 2021; 34:108753. [PMID: 33596422 PMCID: PMC7945993 DOI: 10.1016/j.celrep.2021.108753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/14/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Mutations in the genes encoding the lysine demethylase 5 (KDM5) family of histone demethylases are observed in individuals with intellectual disability (ID). Despite clear evidence linking KDM5 function to neurodevelopmental pathways, how this family of proteins impacts transcriptional programs to mediate synaptic structure and activity remains unclear. Using the Drosophila larval neuromuscular junction (NMJ), we show that KDM5 is required presynaptically for neuroanatomical development and synaptic function. The Jumonji C (JmjC) domain-encoded histone demethylase activity of KDM5, which is expected to be diminished by many ID-associated alleles, is required for appropriate synaptic morphology and neurotransmission. The activity of the C5HC2 zinc finger is also required, as an ID-associated mutation in this motif reduces NMJ bouton number, increases bouton size, and alters microtubule dynamics. KDM5 therefore uses demethylase-dependent and independent mechanisms to regulate NMJ structure and activity, highlighting the complex nature by which this chromatin modifier carries out its neuronal gene-regulatory programs.
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Affiliation(s)
- Helen M Belalcazar
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Emily L Hendricks
- Department of Biological Sciences, Southern Illinois University Edwardsville, 44 Circle Drive, Edwardsville, IL 62026, USA
| | - Sumaira Zamurrad
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Faith L W Liebl
- Department of Biological Sciences, Southern Illinois University Edwardsville, 44 Circle Drive, Edwardsville, IL 62026, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA.
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21
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Saul D, Kosinsky RL. Epigenetics of Aging and Aging-Associated Diseases. Int J Mol Sci 2021; 22:ijms22010401. [PMID: 33401659 PMCID: PMC7794926 DOI: 10.3390/ijms22010401] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/19/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
Aging represents the multifactorial decline in physiological function of every living organism. Over the past decades, several hallmarks of aging have been defined, including epigenetic deregulation. Indeed, multiple epigenetic events were found altered across different species during aging. Epigenetic changes directly contributing to aging and aging-related diseases include the accumulation of histone variants, changes in chromatin accessibility, loss of histones and heterochromatin, aberrant histone modifications, and deregulated expression/activity of miRNAs. As a consequence, cellular processes are affected, which results in the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, and neurodegenerative disorders. In this review, we focus on epigenetic mechanisms underlying aging-related processes in various species and describe how these deregulations contribute to human diseases.
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Affiliation(s)
- Dominik Saul
- Kogod Center on Aging and Division of Endocrinology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of Trauma, Orthopedics and Reconstructive Surgery, Georg-August-University of Goettingen, 37075 Goettingen, Germany
| | - Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-293-2386
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22
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Zhang F, Icyuz M, Bartke A, Sun LY. The effects of early-life growth hormone intervention on tissue specific histone H3 modifications in long-lived Ames dwarf mice. Aging (Albany NY) 2020; 13:1633-1648. [PMID: 33378746 PMCID: PMC7880366 DOI: 10.18632/aging.202451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 11/25/2022]
Abstract
Histone modifications, specifically in the lysine residues of histone H3, have been implicated in lifespan regulation in several model organisms. Our previous studies showed that growth hormone (GH) treatment during early life can dramatically influence lifespan in long-lived Ames dwarf mice. However, the effects of this hormonal intervention on epigenetic modifications have never been examined. In this study, we sought to compare tissue-specific histone H3 lysine methylation and acetylation markers in Ames dwarf and wild type (WT) mice and to determine how these markers are affected by early-life GH intervention. Ames dwarf mice exhibited suppressed H3K4me in both hepatic and brain tissues, while showing elevated H3K27me in the brain. Early-life GH intervention significantly altered the histone H3 markers in those tissues. Furthermore, early GH intervention increased expression of histone H3 acetylation at multiple lysine residues in a tissue-specific manner. This included changes in H3K14ac and H3K18ac in the liver and brain, H3K18ac in visceral adipose tissue and H3K9ac, H3K14ac and H3K27ac in subcutaneous adipose tissue. This study serves as an initial, but important step in elucidating the epigenetic mechanisms by which hormonal signals during early life can influence aging and longevity in mammals.
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Affiliation(s)
- Fang Zhang
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35254, USA
| | - Mert Icyuz
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35254, USA
| | - Andrzej Bartke
- Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
| | - Liou Y. Sun
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35254, USA
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23
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Yi SJ, Kim K. New Insights into the Role of Histone Changes in Aging. Int J Mol Sci 2020; 21:ijms21218241. [PMID: 33153221 PMCID: PMC7662996 DOI: 10.3390/ijms21218241] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Aging is the progressive decline or loss of function at the cellular, tissue, and organismal levels that ultimately leads to death. A number of external and internal factors, including diet, exercise, metabolic dysfunction, genome instability, and epigenetic imbalance, affect the lifespan of an organism. These aging factors regulate transcriptome changes related to the aging process through chromatin remodeling. Many epigenetic regulators, such as histone modification, histone variants, and ATP-dependent chromatin remodeling factors, play roles in chromatin reorganization. The key to understanding the role of gene regulatory networks in aging lies in characterizing the epigenetic regulators responsible for reorganizing and potentiating particular chromatin structures. This review covers epigenetic studies on aging, discusses the impact of epigenetic modifications on gene expression, and provides future directions in this area.
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Kirtana R, Manna S, Patra SK. Molecular mechanisms of KDM5A in cellular functions: Facets during development and disease. Exp Cell Res 2020; 396:112314. [PMID: 33010254 DOI: 10.1016/j.yexcr.2020.112314] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 12/12/2022]
Abstract
Gene expression is influenced at many layers by a fine-tuned crosstalk between multiple extrinsic signalling pathways and intrinsic regulatory molecules that respond to environmental stimuli. Epigenetic modifiers like DNA methyltransferases, histone modifying enzymes and chromatin remodellers are reported to act as triggering factors in many scenarios by exhibiting their control over most of the cellular processes. These epigenetic players can either directly regulate gene expression or interact with some effector molecules that harmonize the expression of downstream genes. One such epigenetic regulator which exhibits multifaceted regulation over gene expression is KDM5A. It is classically a transcriptional repressor acting as H3K4me3 demethylase, but also is reported to act as an activator in many contexts either by loss of activity due to inhibition manifested by other interacting proteins or by downregulating the negative players of a given physiological process thereby escalating the framework. Through this review, we draw attention to the remarkable modes of functioning laid by KDM5A on transcriptional and translational processes, affecting gene expression during differentiation and development and finally summing up on role in disease causation (Fig. 1). We also shed light on different orthologs of KDM5A and their organism specific roles, along with comparison of the sequence similarity to extrapolate some unanswered questions about this protein.
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Affiliation(s)
- R Kirtana
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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25
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Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
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Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA,Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA,Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
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26
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Torres-Campana D, Kimura S, Orsi GA, Horard B, Benoit G, Loppin B. The Lid/KDM5 histone demethylase complex activates a critical effector of the oocyte-to-zygote transition. PLoS Genet 2020; 16:e1008543. [PMID: 32134927 PMCID: PMC7058283 DOI: 10.1371/journal.pgen.1008543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Following fertilization of a mature oocyte, the formation of a diploid zygote involves a series of coordinated cellular events that ends with the first embryonic mitosis. In animals, this complex developmental transition is almost entirely controlled by maternal gene products. How such a crucial transcriptional program is established during oogenesis remains poorly understood. Here, we have performed an shRNA-based genetic screen in Drosophila to identify genes required to form a diploid zygote. We found that the Lid/KDM5 histone demethylase and its partner, the Sin3A-HDAC1 deacetylase complex, are necessary for sperm nuclear decompaction and karyogamy. Surprisingly, transcriptomic analyses revealed that these histone modifiers are required for the massive transcriptional activation of deadhead (dhd), which encodes a maternal thioredoxin involved in sperm chromatin remodeling. Unexpectedly, while lid knock-down tends to slightly favor the accumulation of its target, H3K4me3, on the genome, this mark was lost at the dhd locus. We propose that Lid/KDM5 and Sin3A cooperate to establish a local chromatin environment facilitating the unusually high expression of dhd, a key effector of the oocyte-to-zygote transition. Nuclear enzymes that add or remove epigenetic marks on histone tails potentially control gene expression by affecting chromatin structure and DNA accessibility. For instance, members of the KDM5 family of histone demethylases specifically remove methyl groups on the lysine 4 of histone H3, a mark generally correlated with gene expression. Lid (Little imaginal discs), the Drosophila KDM5, is essential for viability but is also required for female fertility. In this paper, we have found that the specific removal of Lid in developing oocytes perturbs the decompaction of the sperm nucleus at fertilization and the integration of paternal chromosomes in the zygote. Sperm nuclear decompaction normally requires the presence of a small redox protein called Deadhead (Dhd), which is massively expressed at the end of oogenesis. Strikingly, our analyses of ovarian transcriptomes revealed that the absence of Lid completely abolishes the expression of dhd. This direct functional link between a general histone modifier and the expression of an essential terminal effector gene represents a rare finding. We hope that our work will help understanding how histone demethylases function in controlling complex developmental transitions as well as cancer progression.
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Affiliation(s)
- Daniela Torres-Campana
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR5239, Ecole Normale Supérieure de Lyon, University of Lyon, France
| | - Shuhei Kimura
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne F-69622, France
| | - Guillermo A. Orsi
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR5239, Ecole Normale Supérieure de Lyon, University of Lyon, France
| | - Béatrice Horard
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR5239, Ecole Normale Supérieure de Lyon, University of Lyon, France
| | - Gérard Benoit
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR5239, Ecole Normale Supérieure de Lyon, University of Lyon, France
| | - Benjamin Loppin
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR5239, Ecole Normale Supérieure de Lyon, University of Lyon, France
- * E-mail:
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27
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Yu R, McCauley B, Dang W. Loss of chromatin structural integrity is a source of stress during aging. Hum Genet 2020; 139:371-380. [PMID: 31900586 DOI: 10.1007/s00439-019-02100-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/09/2019] [Indexed: 12/19/2022]
Abstract
Dysfunction and dysregulation at multiple levels, from organismal to molecular, are associated with the biological process of aging. In a eukaryotic nucleus, multiple lines of evidence have shown that the fundamental structure of chromatin is affected by aging. Not only euchromatic and heterochromatic regions shift locations, global changes, such as reduced levels of histones, have been reported for certain aged cell types and tissues. The physiological effects caused by such broad chromatin changes are complex and the cell's responses to it can be profound and in turn influence the aging process. In this review, we summarize recent findings on the interplay between chromatin architecture and aging with an emphasis on the cellular response to chromatin stress and its antagonistic effects on aging.
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Affiliation(s)
- Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, 77030, USA
| | - Brenna McCauley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, 77030, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, USA. .,Huffington Center on Aging, Baylor College of Medicine, Houston, 77030, USA.
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28
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Bamodu O, Chao TY. Dissecting the functional pleiotropism of lysine demethylase 5B in physiology and pathology. JOURNAL OF CANCER RESEARCH AND PRACTICE 2020. [DOI: 10.4103/jcrp.jcrp_5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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29
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Drelon C, Rogers MF, Belalcazar HM, Secombe J. The histone demethylase KDM5 controls developmental timing in Drosophila by promoting prothoracic gland endocycles. Development 2019; 146:dev.182568. [PMID: 31862793 PMCID: PMC6955219 DOI: 10.1242/dev.182568] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
In Drosophila, the larval prothoracic gland integrates nutritional status with developmental signals to regulate growth and maturation through the secretion of the steroid hormone ecdysone. While the nutritional signals and cellular pathways that regulate prothoracic gland function are relatively well studied, the transcriptional regulators that orchestrate the activity of this tissue remain less characterized. Here, we show that lysine demethylase 5 (KDM5) is essential for prothoracic gland function. Indeed, restoring kdm5 expression only in the prothoracic gland in an otherwise kdm5 null mutant animal is sufficient to rescue both the larval developmental delay and the pupal lethality caused by loss of KDM5. Our studies show that KDM5 functions by promoting the endoreplication of prothoracic gland cells, a process that increases ploidy and is rate limiting for the expression of ecdysone biosynthetic genes. Molecularly, we show that KDM5 activates the expression of the receptor tyrosine kinase torso, which then promotes polyploidization and growth through activation of the MAPK signaling pathway. Taken together, our studies provide key insights into the biological processes regulated by KDM5 and expand our understanding of the transcriptional regulators that coordinate animal development. Summary: Identification of KDM5 as a new transcriptional regulator of the MAPK signaling cascade provides insights into the molecular mechanisms governing the regulation of ecdysone production and developmental growth control.
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Affiliation(s)
- Coralie Drelon
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Michael F Rogers
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Helen M Belalcazar
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA .,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA
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30
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Parkhitko AA, Jouandin P, Mohr SE, Perrimon N. Methionine metabolism and methyltransferases in the regulation of aging and lifespan extension across species. Aging Cell 2019; 18:e13034. [PMID: 31460700 PMCID: PMC6826121 DOI: 10.1111/acel.13034] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 12/20/2022] Open
Abstract
Methionine restriction (MetR) extends lifespan across different species and exerts beneficial effects on metabolic health and inflammatory responses. In contrast, certain cancer cells exhibit methionine auxotrophy that can be exploited for therapeutic treatment, as decreasing dietary methionine selectively suppresses tumor growth. Thus, MetR represents an intervention that can extend lifespan with a complementary effect of delaying tumor growth. Beyond its function in protein synthesis, methionine feeds into complex metabolic pathways including the methionine cycle, the transsulfuration pathway, and polyamine biosynthesis. Manipulation of each of these branches extends lifespan; however, the interplay between MetR and these branches during regulation of lifespan is not well understood. In addition, a potential mechanism linking the activity of methionine metabolism and lifespan is regulation of production of the methyl donor S-adenosylmethionine, which, after transferring its methyl group, is converted to S-adenosylhomocysteine. Methylation regulates a wide range of processes, including those thought to be responsible for lifespan extension by MetR. Although the exact mechanisms of lifespan extension by MetR or methionine metabolism reprogramming are unknown, it may act via reducing the rate of translation, modifying gene expression, inducing a hormetic response, modulating autophagy, or inducing mitochondrial function, antioxidant defense, or other metabolic processes. Here, we review the mechanisms of lifespan extension by MetR and different branches of methionine metabolism in different species and the potential for exploiting the regulation of methyltransferases to delay aging.
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Affiliation(s)
- Andrey A. Parkhitko
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
| | - Patrick Jouandin
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
| | - Stephanie E. Mohr
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
| | - Norbert Perrimon
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
- Howard Hughes Medical InstituteBostonMassachusetts
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31
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The Epigenetics of Aging in Invertebrates. Int J Mol Sci 2019; 20:ijms20184535. [PMID: 31540238 PMCID: PMC6769462 DOI: 10.3390/ijms20184535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/03/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022] Open
Abstract
Aging is an unstoppable process coupled to the loss of physiological function and increased susceptibility to diseases. Epigenetic alteration is one of the hallmarks of aging, which involves changes in DNA methylation patterns, post-translational modification of histones, chromatin remodeling and non-coding RNA interference. Invertebrate model organisms, such as Drosophila melanogaster and Caenorhabditis elegans, have been used to investigate the biological mechanisms of aging because they show, evolutionarily, the conservation of many aspects of aging. In this review, we focus on recent advances in the epigenetic changes of aging with invertebrate models, providing insight into the relationship between epigenetic dynamics and aging.
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Bachleitner S, Sørensen JL, Gacek-Matthews A, Sulyok M, Studt L, Strauss J. Evidence of a Demethylase-Independent Role for the H3K4-Specific Histone Demethylases in Aspergillus nidulans and Fusarium graminearum Secondary Metabolism. Front Microbiol 2019; 10:1759. [PMID: 31456754 PMCID: PMC6700381 DOI: 10.3389/fmicb.2019.01759] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Fungi produce a plethora of secondary metabolites (SMs) involved in cellular protection, defense, and signaling. Like other metabolic processes, transcription of SM biosynthesis genes is tightly regulated to prevent an unnecessary use of resources. Genes involved in SM biosynthesis are usually physically linked, arranged in secondary metabolite gene clusters (SMGCs). Research over the last decades has shown that chromatin structure and posttranslational modifications (PTMs) of histones represent important layers of SMGC regulation. For instance, trimethylation of histone H3 lysine 4 (H3K4me3) is a PTM typically associated with promoter regions of actively transcribed genes. Previously, we have shown that the H3K4me3-specific, JmjC domain-containing histone demethylase KdmB functions not only in repression but also in activation of secondary metabolism in Aspergillus nidulans, suggesting that KdmB has additional functions apart from histone demethylation. In this study, we identified demethylase-independent functions of KdmB in transcriptional regulation of SM gene clusters. Furthermore, we show that this activating and demethylase-independent role of the H3K4 demethylase is also conserved in the phytopathogenic fungus Fusarium graminearum. Lack of FgKdm5 resulted in significant downregulation of five of seven analyzed SMs, whereby only one SMGC depends on a functional JmjC-domain. In A. nidulans strains deficient in H3K4 methylation, i.e., cclA∆, largely phenocopied kdmB∆, while this is not the case for most of the SMs analyzed in Fusarium spp. Notably, KdmB could not rescue the demethylase function in ∆fgkdm5 but restored all demethylase-independent phenotypes.
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Affiliation(s)
- Simone Bachleitner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Jens Laurids Sørensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Agnieszka Gacek-Matthews
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Michael Sulyok
- Department for Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
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Shimoda H, Doi S, Nakashima A, Sasaki K, Doi T, Masaki T. Inhibition of the H3K4 methyltransferase MLL1/WDR5 complex attenuates renal senescence in ischemia reperfusion mice by reduction of p16 INK4a. Kidney Int 2019; 96:1162-1175. [PMID: 31570196 DOI: 10.1016/j.kint.2019.06.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/19/2022]
Abstract
Renal function declines with aging and is pathologically characterized by chronic inflammation and fibrosis. Renal senescence is induced not only by aging but also by various stimuli, including ischemia reperfusion injury. Recently, the accumulation of p16INK4a-positive cells in the kidney has been considered a molecular feature of renal senescence, with the p16INK4a gene reportedly regulated by mixed-lineage leukemia 1 (MLL1)/WD-40 repeat protein 5 (WDR5)-mediated histone 3 lysine 4 trimethylation (H3K4me3). Here, we determined whether inhibition of MLL1/WDR5 activity attenuates renal senescence, inflammation, and fibrosis in mice with ischemia reperfusion injury and in cultured rat renal fibroblasts. MM-102 or OICR-9429, both MLL1/WDR5 protein-protein interaction inhibitors, and small interfering RNA (siRNA) for MLL1 or WDR5 suppressed the expression of p16INK4a in mice with ischemia reperfusion injury, accompanied by downregulation of H3K4me3 expression. MM-102 attenuated renal fibrosis and inflammation in the kidney of mice with ischemia reperfusion injury. Moreover, in vitro study showed that transforming growth factor-β1 induced the expression of MLL1, WDR5, H3K4me3, and p16INK4a. Finally, chromatin immunoprecipitation identified the p16INK4a promoter at an H3K4me3 site in renal fibroblasts. Thus, our findings show that H3K4me3 inhibition ameliorates ischemia reperfusion-induced renal senescence along with fibrosis and inflammation.
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Affiliation(s)
- Hironori Shimoda
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Shigehiro Doi
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan.
| | - Ayumu Nakashima
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Kensuke Sasaki
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Toshiki Doi
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Takao Masaki
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan.
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Romero-Bueno R, de la Cruz Ruiz P, Artal-Sanz M, Askjaer P, Dobrzynska A. Nuclear Organization in Stress and Aging. Cells 2019; 8:cells8070664. [PMID: 31266244 PMCID: PMC6678840 DOI: 10.3390/cells8070664] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/23/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic nucleus controls most cellular processes. It is isolated from the cytoplasm by the nuclear envelope, which plays a prominent role in the structural organization of the cell, including nucleocytoplasmic communication, chromatin positioning, and gene expression. Alterations in nuclear composition and function are eminently pronounced upon stress and during premature and physiological aging. These alterations are often accompanied by epigenetic changes in histone modifications. We review, here, the role of nuclear envelope proteins and histone modifiers in the 3-dimensional organization of the genome and the implications for gene expression. In particular, we focus on the nuclear lamins and the chromatin-associated protein BAF, which are linked to Hutchinson–Gilford and Nestor–Guillermo progeria syndromes, respectively. We also discuss alterations in nuclear organization and the epigenetic landscapes during normal aging and various stress conditions, ranging from yeast to humans.
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Affiliation(s)
- Raquel Romero-Bueno
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
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35
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Zamurrad S, Hatch HAM, Drelon C, Belalcazar HM, Secombe J. A Drosophila Model of Intellectual Disability Caused by Mutations in the Histone Demethylase KDM5. Cell Rep 2019; 22:2359-2369. [PMID: 29490272 DOI: 10.1016/j.celrep.2018.02.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 12/08/2017] [Accepted: 02/05/2018] [Indexed: 10/17/2022] Open
Abstract
Mutations in KDM5 family histone demethylases cause intellectual disability in humans. However, the molecular mechanisms linking KDM5-regulated transcription and cognition remain unknown. Here, we establish Drosophila as a model to understand this connection by generating a fly strain harboring an allele analogous to a disease-causing missense mutation in human KDM5C (kdm5A512P). Transcriptome analysis of kdm5A512P flies revealed a striking downregulation of genes required for ribosomal assembly and function and a concomitant reduction in translation. kdm5A512P flies also showed impaired learning and/or memory. Significantly, the behavioral and transcriptional changes in kdm5A512P flies were similar to those specifically lacking demethylase activity. These data suggest that the primary defect of the KDM5A512P mutation is a loss of histone demethylase activity and reveal an unexpected role for this enzymatic function in gene activation. Because translation is critical for neuronal function, we propose that this defect contributes to the cognitive defects of kdm5A512P flies.
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Affiliation(s)
- Sumaira Zamurrad
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA
| | - Coralie Drelon
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Helen M Belalcazar
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA.
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36
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Lewis L, Borowa-Mazgaj B, de Conti A, Chappell GA, Luo YS, Bodnar W, Konganti K, Wright FA, Threadgill DW, Chiu WA, Pogribny IP, Rusyn I. Population-Based Analysis of DNA Damage and Epigenetic Effects of 1,3-Butadiene in the Mouse. Chem Res Toxicol 2019; 32:887-898. [PMID: 30990016 DOI: 10.1021/acs.chemrestox.9b00035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metabolism of 1,3-butadiene, a known human and rodent carcinogen, results in formation of reactive epoxides, a key event in its carcinogenicity. Although mice exposed to 1,3-butadiene present DNA adducts in all tested tissues, carcinogenicity is limited to liver, lung, and lymphoid tissues. Previous studies demonstrated that strain- and tissue-specific epigenetic effects in response to 1,3-butadiene exposure may influence susceptibly to DNA damage and serve as a potential mechanism of tissue-specific carcinogenicity. This study aimed to investigate interindividual variability in the effects of 1,3-butadiene using a population-based mouse model. Male mice from 20 Collaborative Cross strains were exposed to 0 or 635 ppm 1,3-butadiene by inhalation (6 h/day, 5 days/week) for 2 weeks. We evaluated DNA damage and epigenetic effects in target (lung and liver) and nontarget (kidney) tissues of 1,3-butadiene-induced carcinogenesis. DNA damage was assessed by measuring N-7-(2,3,4-trihydroxybut-1-yl)-guanine (THB-Gua) adducts. To investigate global histone modification alterations, we evaluated the trimethylation and acetylation of histones H3 and H4 across tissues. Changes in global cytosine DNA methylation were evaluated from the levels of methylation of LINE-1 and SINE B1 retrotransposons. We quantified the degree of variation across strains, deriving a chemical-specific human variability factor to address population variability in carcinogenic risk, which is largely ignored in current cancer risk assessment practice. Quantitative trait locus mapping identified four candidate genes related to chromatin remodeling whose variation was associated with interstrain susceptibility. Overall, this study uses 1,3-butadiene to demonstrate how the Collaborative Cross mouse population can be used to identify the mechanisms for and quantify the degree of interindividual variability in tissue-specific effects that are relevant to chemically induced carcinogenesis.
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Affiliation(s)
- Lauren Lewis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Barbara Borowa-Mazgaj
- Division of Biochemical Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas 72079 , United States
| | - Aline de Conti
- Division of Biochemical Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas 72079 , United States
| | - Grace A Chappell
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Yu-Syuan Luo
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Wanda Bodnar
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27516 , United States
| | - Kranti Konganti
- Department of Molecular and Cellular Medicine, College of Medicine , Texas A&M University , College Station , Texas 77843-1114 , United States
| | - Fred A Wright
- Bioinformatics Research Center , North Carolina State University , Raleigh , North Carolina 27695-7566 , United States
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, College of Medicine , Texas A&M University , College Station , Texas 77843-1114 , United States
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Igor P Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas 72079 , United States
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
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37
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Molina-Serrano D, Kyriakou D, Kirmizis A. Histone Modifications as an Intersection Between Diet and Longevity. Front Genet 2019; 10:192. [PMID: 30915107 PMCID: PMC6422915 DOI: 10.3389/fgene.2019.00192] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/22/2019] [Indexed: 12/12/2022] Open
Abstract
Histone modifications are key epigenetic regulators that control chromatin structure and gene transcription, thereby impacting on various important cellular phenotypes. Over the past decade, a growing number of studies have indicated that changes in various histone modifications have a significant influence on the aging process. Furthermore, it has been revealed that the abundance and localization of histone modifications are responsive to various environmental stimuli, such as diet, which can also affect gene expression and lifespan. This supports the notion that histone modifications can serve as a main cellular platform for signal integration. Hence, in this review we focus on the role of histone modifications during aging, report the data indicating that diet affects histone modification levels and explore the idea that histone modifications may function as an intersection through which diet regulates lifespan. A greater understanding of the epigenetic mechanisms that link environmental signals to longevity may provide new strategies for therapeutic intervention in age-related diseases and for promoting healthy aging.
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Affiliation(s)
- Diego Molina-Serrano
- UMR 6290, Centre National de la Recherche Scientifique, Rennes, France.,Institute of Genetics and Development of Rennes (IGDR), Université de Rennes 1, Rennes, France
| | - Dimitris Kyriakou
- Efevre Tech Ltd., Larnaca, Cyprus.,Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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38
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Papsdorf K, Brunet A. Linking Lipid Metabolism to Chromatin Regulation in Aging. Trends Cell Biol 2019; 29:97-116. [PMID: 30316636 PMCID: PMC6340780 DOI: 10.1016/j.tcb.2018.09.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022]
Abstract
The lifespan of an organism is strongly influenced by environmental factors (including diet) and by internal factors (notably reproductive status). Lipid metabolism is critical for adaptation to external conditions or reproduction. Interestingly, specific lipid profiles are associated with longevity, and increased uptake of certain lipids extends longevity in Caenorhabditis elegans and ameliorates disease phenotypes in humans. How lipids impact longevity, and how lipid metabolism is regulated during aging, is just beginning to be unraveled. This review describes recent advances in the regulation and role of lipids in longevity, focusing on the interaction between lipid metabolism and chromatin states in aging and age-related diseases.
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Affiliation(s)
- Katharina Papsdorf
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA 94305, USA.
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39
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Liu P, Zhang S, Zhou B, Luo X, Zhou XF, Cai B, Jin YH, Niu D, Lin J, Cao X, Jin JB. The Histone H3K4 Demethylase JMJ16 Represses Leaf Senescence in Arabidopsis. THE PLANT CELL 2019; 31:430-443. [PMID: 30712008 PMCID: PMC6447021 DOI: 10.1105/tpc.18.00693] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/07/2019] [Accepted: 01/27/2019] [Indexed: 05/04/2023]
Abstract
Leaf senescence is governed by a complex regulatory network involving the dynamic reprogramming of gene expression. Age-dependent induction of senescence-associated genes (SAGs) is associated with increased levels of trimethylation of histone H3 at Lys4 (H3K4me3), but the regulatory mechanism remains elusive. Here, we found that JMJ16, an Arabidopsis (Arabidopsis thaliana) JmjC-domain containing protein, is a specific H3K4 demethylase that negatively regulates leaf senescence through its enzymatic activity. Genome-wide analysis revealed a widespread coordinated upregulation of gene expression and hypermethylation of H3K4me3 at JMJ16 binding genes associated with leaf senescence in the loss-of-function jmj16 mutant as compared with the wild type. Genetic analysis indicated that JMJ16 negatively regulates leaf senescence, at least partly through repressing the expression of positive regulators of leaf senescence, WRKY53 and SAG201 JMJ16 associates with WRKY53 and SAG201 and represses their precocious expression in mature leaves by reducing H3K4me3 levels at these loci. The protein abundance of JMJ16 gradually decreases during aging, which is correlated with increased H3K4me3 levels at WRKY53 and SAG201, suggesting that the age-dependent downregulation of JMJ16 is required for the precise transcriptional activation of SAGs during leaf senescence. Thus, JMJ16 is an important regulator of leaf senescence that demethylates H3K4 at SAGs in an age-dependent manner.
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Affiliation(s)
- Peng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shuaibin Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Luo
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xiao Feng Zhou
- Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Bin Cai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yin Hua Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - De Niu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinxing Lin
- China College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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40
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Kane AE, Sinclair DA. Epigenetic changes during aging and their reprogramming potential. Crit Rev Biochem Mol Biol 2019; 54:61-83. [PMID: 30822165 PMCID: PMC6424622 DOI: 10.1080/10409238.2019.1570075] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 02/07/2023]
Abstract
The aging process results in significant epigenetic changes at all levels of chromatin and DNA organization. These include reduced global heterochromatin, nucleosome remodeling and loss, changes in histone marks, global DNA hypomethylation with CpG island hypermethylation, and the relocalization of chromatin modifying factors. Exactly how and why these changes occur is not fully understood, but evidence that these epigenetic changes affect longevity and may cause aging, is growing. Excitingly, new studies show that age-related epigenetic changes can be reversed with interventions such as cyclic expression of the Yamanaka reprogramming factors. This review presents a summary of epigenetic changes that occur in aging, highlights studies indicating that epigenetic changes may contribute to the aging process and outlines the current state of research into interventions to reprogram age-related epigenetic changes.
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Affiliation(s)
- Alice E. Kane
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - David A. Sinclair
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology, The University of New South Wales, Sydney, Australia
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41
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Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG. Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun 2019; 10:94. [PMID: 30626866 PMCID: PMC6327041 DOI: 10.1038/s41467-018-07829-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Histone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer. The in vitro demethylase activity of KDM5A is allosterically enhanced by binding of its product, unmodified H3 peptides, to its PHD1 reader domain. However, the molecular basis of this allosteric enhancement is unclear. Here we show that saturation of the PHD1 domain by the H3 N-terminal tail peptides stabilizes binding of the substrate to the catalytic domain and improves the catalytic efficiency of demethylation. When present in saturating concentrations, differently modified H3 N-terminal tail peptides have a similar effect on demethylation. However, they vary greatly in their affinity towards the PHD1 domain, suggesting that H3 modifications can tune KDM5A activity. Furthermore, hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) experiments reveal conformational changes in the allosterically enhanced state. Our findings may enable future development of anti-cancer therapies targeting regions involved in allosteric regulation. The demethylase activity of KDM5A is allosterically enhanced by binding of histone H3 to its PHD1 reader domain, through an unknown mechanism. Here the authors show that the PHD1 domain drives ligand-induced allosteric stimulation by stabilizing the binding of substrate to the catalytic domain.
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Affiliation(s)
- James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Cynthia M Chio
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | | | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Devrishi Goswami
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Karen Ruiz
- TETRAD Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA. .,Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA.
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42
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Song W, Zsindely N, Faragó A, Marsh JL, Bodai L. Systematic genetic interaction studies identify histone demethylase Utx as potential target for ameliorating Huntington's disease. Hum Mol Genet 2019; 27:649-666. [PMID: 29281014 DOI: 10.1093/hmg/ddx432] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/15/2017] [Indexed: 01/29/2023] Open
Abstract
Huntington's disease (HD) is a dominantly inherited neurodegenerative disease caused by alterations in the huntingtin gene (htt). Transcriptional dysregulation is an early event in HD progression. Protein acetylation and methylation particularly on histones regulates chromatin structure thereby preventing or facilitating transcription. Although protein acetylation has been found to affect HD symptoms, little is known about the potential role of protein methylation in HD pathology. In recent years, a series of proteins have been described that are responsible for methylating and demethylating histones as well as other proteins. We carried out systematic genetic interaction studies testing lysine and arginine methylases and demethylases in a Drosophila melanogaster HD model. We found that modulating methylation enzymes that typically affect histone positions H3K4, H3K36 or H3K79 had varying effects on HD pathology while modulating ones that typically affect constitutive heterochromatin marks at H3K9 and H4K20 generally had limited impact on HD pathology. In contrast, modulating enzymes acting on the facultative heterochromatin mark at H3K27 had specific effects on HD pathology, with reduction of the demethylase Utx rescuing HTT-induced pathology while reducing Polycomb Repressive Complex2 core methylase components led to more aggressive pathology. Further exploration of the mechanism underlying the methylation-specific interactions suggest that these lysine and arginine methylases and demethylases are likely exerting their influence through non-histone targets. These results highlight a novel therapeutic approach for HD in the form of Utx inhibition.
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Affiliation(s)
- Wan Song
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Anikó Faragó
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary.,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - J Lawrence Marsh
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA
| | - László Bodai
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA.,Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
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43
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Kishimoto S, Uno M, Nishida E. Molecular mechanisms regulating lifespan and environmental stress responses. Inflamm Regen 2018; 38:22. [PMID: 30555601 PMCID: PMC6287349 DOI: 10.1186/s41232-018-0080-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/22/2022] Open
Abstract
Throughout life, organisms are subjected to a variety of environmental perturbations, including temperature, nutrient conditions, and chemical agents. Exposure to external signals induces diverse changes in the physiological conditions of organisms. Genetically identical individuals exhibit highly phenotypic variations, which suggest that environmental variations among individuals can affect their phenotypes in a cumulative and inhomogeneous manner. The organismal phenotypes mediated by environmental conditions involve development, metabolic pathways, fertility, pathological processes, and even lifespan. It is clear that genetic factors influence the lifespan of organisms. Likewise, it is now increasingly recognized that environmental factors also have a large impact on the regulation of aging. Multiple studies have reported on the contribution of epigenetic signatures to the long-lasting phenotypic effects induced by environmental signals. Nevertheless, the mechanism of how environmental stimuli induce epigenetic changes at specific loci, which ultimately elicit phenotypic variations, is still largely unknown. Intriguingly, in some cases, the altered phenotypes associated with epigenetic changes could be stably passed on to the next generations. In this review, we discuss the environmental regulation of organismal viability, that is, longevity and stress resistance, and the relationship between this regulation and epigenetic factors, focusing on studies in the nematode C. elegans.
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Affiliation(s)
- Saya Kishimoto
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047 Japan.,2Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Masaharu Uno
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047 Japan.,2Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Eisuke Nishida
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe, 650-0047 Japan.,2Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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44
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Systematic Analysis of SIN3 Histone Modifying Complex Components During Development. Sci Rep 2018; 8:17048. [PMID: 30451916 PMCID: PMC6242963 DOI: 10.1038/s41598-018-35093-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022] Open
Abstract
Establishment and maintenance of histone acetylation levels are critical for metazoan development and viability. Disruption of the balance between acetylation and deacetylation by treatment with chemical histone deacetylase (HDAC) inhibitors results in loss of cell proliferation, differentiation and/or apoptosis. Histone deacetylation by the SIN3 complex is essential in Drosophila and mice, as loss of the scaffolding factor SIN3 or the associated HDAC results in lethality. The objective of this study is to elucidate contributions of SIN3 complex components to these essential processes. We used the Drosophila model organism to carry out a systematic functional analysis of the SIN3 complex. We find that SIN3 associated proteins are essential for viability and cell proliferation during development. Additionally, tissue specific reduction of SIN3 complex components results in abnormal wing development. Interestingly, while knockdown of each factor resulted in similar phenotypes, their individual effects on recruitment of SIN3 to polytene chromosomes are distinct. Reduction of some factors leads to large changes in the morphology of the chromosome and/or greatly reduced SIN3 binding. These findings suggest that while individual SIN3 complex components work through distinct molecular mechanisms, they each make a substantial contribution to the overall function of this highly conserved histone deacetylase complex.
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45
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Affiliation(s)
- Jung-Ae Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, South Korea
| | - Minjung Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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46
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Cruz C, Della Rosa M, Krueger C, Gao Q, Horkai D, King M, Field L, Houseley J. Tri-methylation of histone H3 lysine 4 facilitates gene expression in ageing cells. eLife 2018; 7:34081. [PMID: 30274593 PMCID: PMC6168286 DOI: 10.7554/elife.34081] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 09/17/2018] [Indexed: 12/21/2022] Open
Abstract
Transcription of protein coding genes is accompanied by recruitment of COMPASS to promoter-proximal chromatin, which methylates histone H3 lysine 4 (H3K4) to form H3K4me1, H3K4me2 and H3K4me3. Here, we determine the importance of COMPASS in maintaining gene expression across lifespan in budding yeast. We find that COMPASS mutations reduce replicative lifespan and cause expression defects in almost 500 genes. Although H3K4 methylation is reported to act primarily in gene repression, particularly in yeast, repressive functions are progressively lost with age while hundreds of genes become dependent on H3K4me3 for full expression. Basal and inducible expression of these genes is also impaired in young cells lacking COMPASS components Swd1 or Spp1. Gene induction during ageing is associated with increasing promoter H3K4me3, but H3K4me3 also accumulates in non-promoter regions and the ribosomal DNA. Our results provide clear evidence that H3K4me3 is required to maintain normal expression of many genes across organismal lifespan.
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Affiliation(s)
- Cristina Cruz
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Monica Della Rosa
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Christel Krueger
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Qian Gao
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Dorottya Horkai
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Michelle King
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Lucy Field
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Houseley
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
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47
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Zheng Y, Xue Y, Ren X, Liu M, Li X, Jia Y, Niu Y, Ni JQ, Zhang Y, Ji JY. The Lysine Demethylase dKDM2 Is Non-essential for Viability, but Regulates Circadian Rhythms in Drosophila. Front Genet 2018; 9:354. [PMID: 30233643 PMCID: PMC6131532 DOI: 10.3389/fgene.2018.00354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/15/2018] [Indexed: 12/29/2022] Open
Abstract
Post-translational modification of histones, such as histone methylation controlled by specific methyltransferases and demethylases, play critical roles in modulating chromatin dynamics and transcription in eukaryotes. Misregulation of histone methylation can lead to aberrant gene expression, thereby contributing to abnormal development and diseases such as cancer. As such, the mammalian lysine-specific demethylase 2 (KDM2) homologs, KDM2A and KDM2B, are either oncogenic or tumor suppressive depending on specific pathological contexts. However, the role of KDM2 proteins during development remains poorly understood. Unlike vertebrates, Drosophila has only one KDM2 homolog (dKDM2), but its functions in vivo remain elusive due to the complexities of the existing mutant alleles. To address this problem, we have generated two dKdm2 null alleles using the CRISPR/Cas9 technique. These dKdm2 homozygous mutants are fully viable and fertile, with no developmental defects observed under laboratory conditions. However, the dKdm2 null mutant adults display defects in circadian rhythms. Most of the dKdm2 mutants become arrhythmic under constant darkness, while the circadian period of the rhythmic mutant flies is approximately 1 h shorter than the control. Interestingly, lengthened circadian periods are observed when dKDM2 is overexpressed in circadian pacemaker neurons. Taken together, these results demonstrate that dKdm2 is not essential for viability; instead, dKDM2 protein plays important roles in regulating circadian rhythms in Drosophila. Further analyses of the molecular mechanisms of dKDM2 and its orthologs in vertebrates regarding the regulation of circadian rhythms will advance our understanding of the epigenetic regulations of circadian clocks.
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Affiliation(s)
- Yani Zheng
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
| | - Yongbo Xue
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Xingjie Ren
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
| | - Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
| | - Yu Jia
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Ye Niu
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Jian-Quan Ni
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
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Varma P, Mishra RK. Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos. J Biosci 2018; 43:621-633. [PMID: 30207309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nuclear Matrix (NuMat) is the structural and functional framework of the nucleus. It has been shown that attachment of chromatin to NuMat brings significant regulation of the transcriptional activity of particular genes; however, key components of NuMat involved in this process remain elusive. We have identified Lid (Little imaginal discs) as one of the components of NuMat. It belongs to the TrxG group of proteins involved in activation of important developmental genes. However, unlike other activator proteins of TrxG, Lid is a Jumonji protein involved in H3K4me3 demethylation. Here, we report the association of Lid and its various domains with NuMat which implicates its structural role in chromatin organization and epigenetic basis of cellular memory. We have found that both N and C terminal regions of this protein are capable of associating with NuMat. We have further mapped the association of individual domains and found that, PHD, ARID and JmjC domains can associate with NuMat individually. Moreover, deletion of N-terminal PHD finger does not alter Lid's NuMat association implying that although it is sufficient, yet, it is not necessary for Lid's structural role in NuMat. Based on our findings, we hypothesize that C terminal region of Lid which contains PHD fingers might be responsible for its NuMat association via protein-DNA interactions. However, for the N terminal region harboring both a PHD and an ARID finger, Lid anchors to the NuMat via both protein-protein and protein-DNA interactions. The association of JmjC domain with NuMat is the first report of the association of a demethylase domain with NuMat suggesting that Lid, a demethylase, being part of NuMat might be involved in regulating the chromatin dynamics via its NuMat association.
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Affiliation(s)
- Parul Varma
- CSIR - Center for Cellular and Molecular Biology, Hyderabad 500 007, India
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49
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Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos. J Biosci 2018. [DOI: 10.1007/s12038-018-9773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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50
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Ramirez-Roman ME, Billini CE, Ghezzi A. Epigenetic Mechanisms of Alcohol Neuroadaptation: Insights from Drosophila. J Exp Neurosci 2018; 12:1179069518779809. [PMID: 29899666 PMCID: PMC5990879 DOI: 10.1177/1179069518779809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022] Open
Abstract
Alcohol addiction is a serious condition perpetuated by enduring physiological and behavioral adaptations. An important component of these adaptations is the long-term rearrangement of neuronal gene expression in the brain of the addicted individual. Epigenetic histone modifications have recently surfaced as important modulators of the transcriptional adaptation to alcohol as these are thought to represent a form of transcriptional memory that is directly imprinted on the chromosome. Some histone modifications affect transcription by modulating the accessibility of the underlying DNA, whereas others have been proposed to serve as marks read by transcription factors as a "histone code" that helps to specify the expression level of a gene. Although the effects of some epigenetic modifications on the transcriptional activity of genes are well known, the mechanisms by which alcohol consumption produces this rearrangement and leads to lasting changes in behavior remain unresolved. Recent advances using the Drosophila model system have started to unravel the epigenetic modulators underlying functional alcohol neuroadaptations. In this review, we discuss the role of 3 different histone modification systems in Drosophila, which have a direct impact on key alcohol neuroadaptations associated with the addictive process. These systems involve the histone deacetylase Sirt1, the histone acetyltransferase CREB-binding protein (CBP), and a subset of the Drosophila JmjC-Domain histone demethylase family.
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Affiliation(s)
| | - Carlos E Billini
- Department of Biology, University of Puerto Rico–Rio Piedras, San Juan, PR, USA
| | - Alfredo Ghezzi
- Department of Biology, University of Puerto Rico–Rio Piedras, San Juan, PR, USA
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