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Miller WB, Baluška F, Reber AS, Slijepčević P. Why death and aging ? All memories are imperfect. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 187:21-35. [PMID: 38316274 DOI: 10.1016/j.pbiomolbio.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/02/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Recent papers have emphasized the primary role of cellular information management in biological and evolutionary development. In this framework, intelligent cells collectively measure environmental cues to improve informational validity to support natural cellular engineering as collaborative decision-making and problem-solving in confrontation with environmental stresses. These collective actions are crucially dependent on cell-based memories as acquired patterns of response to environmental stressors. Notably, in a cellular self-referential framework, all biological information is ambiguous. This conditional requirement imposes a previously unexplored derivative. All cellular memories are imperfect. From this atypical background, a novel theory of aging and death is proposed. Since cellular decision-making is memory-dependent and biology is a continuous natural learning system, the accumulation of previously acquired imperfect memories eventually overwhelms the flexibility cells require to react adroitly to contemporaneous stresses to support continued cellular homeorhetic balance. The result is a gradual breakdown of the critical ability to efficiently measure environmental information and effect cell-cell communication. This age-dependent accretion governs senescence, ultimately ending in death as an organism-wide failure of cellular networking. This approach to aging and death is compatible with all prior theories. Each earlier approach illuminates different pertinent cellular signatures of this ongoing, obliged, living process.
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Affiliation(s)
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Germany.
| | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada.
| | - Predrag Slijepčević
- Department of Life Sciences, College of Health, Medicine and Life Sciences, University of Brunel, UK.
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2
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Jin L, He J, Feng H, Li S, Liu H, Dong H, Hu M, Huang J, Wu H, Chen J, Qi L, Wu K. Transposable elements activation triggers necroptosis in mouse embryonic stem cells. Cell Death Dis 2023; 14:184. [PMID: 36882393 PMCID: PMC9992707 DOI: 10.1038/s41419-023-05705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023]
Abstract
Deficiency of the histone H3K9 methyltransferase SETDB1 induces RIPK3-dependent necroptosis in mouse embryonic stem cells (mESCs). However, how necroptosis pathway is activated in this process remains elusive. Here we report that the reactivation of transposable elements (TEs) upon SETDB1 knockout is responsible for the RIPK3 regulation through both cis and trans mechanisms. IAPLTR2_Mm and MMERVK10c-int, both of which are suppressed by SETDB1-dependent H3K9me3, act as enhancer-like cis-regulatory elements and their RIPK3 nearby members enhance RIPK3 expression when SETDB1 is knockout. Moreover, reactivated endogenous retroviruses generate excessive viral mimicry, which promotes necroptosis mainly through Z-DNA-binding protein 1 (ZBP1). These results indicate TEs play an important role in regulating necroptosis.
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Affiliation(s)
- Lingmei Jin
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China.,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China
| | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China.,Guangzhou Laboratory, Guangzhou, 510005, Guangdong Province, China
| | - Huijian Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sa Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China
| | - Hongzhi Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - MingLi Hu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Junju Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Haoyu Wu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
| | - Ling Qi
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China.
| | - Kaixin Wu
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China. .,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China. .,Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
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3
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Hanselmann S, Gertzmann D, Shin WJ, Ade CP, Gaubatz S. Expression of the cytokinesis regulator PRC1 results in p53-pathway activation in A549 cells but does not directly regulate gene expression in the nucleus. Cell Cycle 2023; 22:419-432. [PMID: 36135961 PMCID: PMC9879178 DOI: 10.1080/15384101.2022.2122258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023] Open
Abstract
Protein regulator of cytokinesis 1 (PRC1) is a microtubule-binding protein with essential roles in mitosis and cytokinesis. PRC1 is frequently overexpressed in cancer cells where it could contribute to chromosomal instability. Due to its nuclear localization in interphase, it has been speculated that PRC1 has additional functions that are involved in its pro-tumorigenic functions. In this study we investigated the potential nuclear functions of PRC1 in a lung cancer cell line. Genome wide expression profiling by RNA sequencing revealed that the expression of PRC1 results in activation of the p53 pathway and inhibition of the pro-proliferative E2F-dependent gene expression. A mutant of PRC1 that is unable to enter into the nucleus regulated the same gene sets as wildtype PRC1, suggesting that PRC1 has no nuclear-exclusive functions in A549 cells. Instead, induction of p53 by PRC1 correlates with multinucleation and depends on the localization of PRC1 to the midbody, suggesting that the induction of p53 is a consequence of overexpressed PRC1 to interfere with the normal function of PRC1 during cytokinesis. Activation of p53 by PRC1 results in cellular senescence but not in apoptosis. In conclusion, while PRC1 is frequently overexpressed in many cancers, the p53 pathways may initially protect cancer cells from the negative effects of PRC1 overexpression on cytokinesis. Because depletion of PRC1 also results in p53-pathway activation and senescence, levels of PRC1 need to be tightly regulated to allow unperturbed proliferation. Targeting the expression or function of PRC1 could create a therapeutic vulnerability for the treatment of cancer.
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Affiliation(s)
- Steffen Hanselmann
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg, Germany
| | - Dörthe Gertzmann
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg, Germany
| | - Woo Jin Shin
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg, Germany
| | - Carsten P. Ade
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg, Germany
| | - Stefan Gaubatz
- Theodor Boveri Institute, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg, Germany
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4
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Miller WB, Enguita FJ, Leitão AL. Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution. Cells 2021; 10:1125. [PMID: 34066959 PMCID: PMC8148535 DOI: 10.3390/cells10051125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 12/16/2022] Open
Abstract
Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.
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Affiliation(s)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal;
| | - Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
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5
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Lewis EMA, Kaushik K, Sandoval LA, Antony I, Dietmann S, Kroll KL. Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid. Neurochem Int 2021; 147:105039. [PMID: 33915225 PMCID: PMC8387070 DOI: 10.1016/j.neuint.2021.105039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 01/22/2023]
Abstract
Epigenetic regulation plays an important role in controlling gene expression during complex processes, such as development of the human brain. Mutations in genes encoding chromatin modifying proteins and in the non-protein coding sequences of the genome can potentially alter transcription factor binding or chromatin accessibility. Such mutations can frequently cause neurodevelopmental disorders, therefore understanding how epigenetic regulation shapes brain development is of particular interest. While epigenetic regulation of neural development has been extensively studied in murine models, significant species-specific differences in both the genome sequence and in brain development necessitate human models. However, access to human fetal material is limited and these tissues cannot be grown or experimentally manipulated ex vivo. Therefore, models that recapitulate particular aspects of human fetal brain development, such as the in vitro differentiation of human pluripotent stem cells (hPSCs), are instrumental for studying the epigenetic regulation of human neural development. Here, we examine recent studies that have defined changes in the epigenomic landscape during fetal brain development. We compare these studies with analogous data derived by in vitro differentiation of hPSCs into specific neuronal cell types or as three-dimensional cerebral organoids. Such comparisons can be informative regarding which aspects of fetal brain development are faithfully recapitulated by in vitro differentiation models and provide a foundation for using experimentally tractable in vitro models of human brain development to study neural gene regulation and the basis of its disruption to cause neurodevelopmental disorders.
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Affiliation(s)
- Emily M A Lewis
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Komal Kaushik
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Luke A Sandoval
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Irene Antony
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
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6
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Ferrari R, Grandi N, Tramontano E, Dieci G. Retrotransposons as Drivers of Mammalian Brain Evolution. Life (Basel) 2021; 11:life11050376. [PMID: 33922141 PMCID: PMC8143547 DOI: 10.3390/life11050376] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Retrotransposons, a large and diverse class of transposable elements that are still active in humans, represent a remarkable force of genomic innovation underlying mammalian evolution. Among the features distinguishing mammals from all other vertebrates, the presence of a neocortex with a peculiar neuronal organization, composition and connectivity is perhaps the one that, by affecting the cognitive abilities of mammals, contributed mostly to their evolutionary success. Among mammals, hominids and especially humans display an extraordinarily expanded cortical volume, an enrichment of the repertoire of neural cell types and more elaborate patterns of neuronal connectivity. Retrotransposon-derived sequences have recently been implicated in multiple layers of gene regulation in the brain, from transcriptional and post-transcriptional control to both local and large-scale three-dimensional chromatin organization. Accordingly, an increasing variety of neurodevelopmental and neurodegenerative conditions are being recognized to be associated with retrotransposon dysregulation. We review here a large body of recent studies lending support to the idea that retrotransposon-dependent evolutionary novelties were crucial for the emergence of mammalian, primate and human peculiarities of brain morphology and function.
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Affiliation(s)
- Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (N.G.); (E.T.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (N.G.); (E.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042 Monserrato, Italy
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
- Correspondence:
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7
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How Chaotic Is Genome Chaos? Cancers (Basel) 2021; 13:cancers13061358. [PMID: 33802828 PMCID: PMC8002653 DOI: 10.3390/cancers13061358] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Cancer genomes can undergo major restructurings involving many chromosomal locations at key stages in tumor development. This restructuring process has been designated “genome chaos” by some authors. In order to examine how chaotic cancer genome restructuring may be, the cell and molecular processes for DNA restructuring are reviewed. Examination of the action of these processes in various cancers reveals a degree of specificity that indicates genome restructuring may be sufficiently reproducible to enable possible therapies that interrupt tumor progression to more lethal forms. Abstract Cancer genomes evolve in a punctuated manner during tumor evolution. Abrupt genome restructuring at key steps in this evolution has been called “genome chaos.” To answer whether widespread genome change is truly chaotic, this review (i) summarizes the limited number of cell and molecular systems that execute genome restructuring, (ii) describes the characteristic signatures of DNA changes that result from activity of those systems, and (iii) examines two cases where genome restructuring is determined to a significant degree by cell type or viral infection. The conclusion is that many restructured cancer genomes display sufficiently unchaotic signatures to identify the cellular systems responsible for major oncogenic transitions, thereby identifying possible targets for therapies to inhibit tumor progression to greater aggressiveness.
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8
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Miller WB, Baluška F, Torday JS. Cellular senomic measurements in Cognition-Based Evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 156:20-33. [PMID: 32738355 DOI: 10.1016/j.pbiomolbio.2020.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/20/2020] [Accepted: 07/04/2020] [Indexed: 12/27/2022]
Abstract
All living entities are cognitive and dependent on ambiguous information. Any assessment of that imprecision is necessarily a measuring function. Individual cells measure information to sustain self-referential homeostatic equipoise (self-identity) in juxtaposition to the external environment. The validity of that information is improved by its collective assessment. The reception of cellular information obliges thermodynamic reactions that initiate a self-reinforcing work channel. This expresses as natural cellular engineering and niche constructions which become the complex interrelated tissue ecologies of holobionts. Multicellularity is collaborative cellular information management directed towards the optimization of information quality through its collective measured assessment. Biology and its evolution can now be re-framed as the continuous process of self-referential cellular measurement in the perpetual defense of individual cellular self-identities through the collective form.
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Affiliation(s)
| | | | - John S Torday
- Department of Pediatrics, Harbor-UCLA Medical Center, USA.
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9
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Gemenetzi M, Lotery AJ. Epigenetics in age-related macular degeneration: new discoveries and future perspectives. Cell Mol Life Sci 2020; 77:807-818. [PMID: 31897542 PMCID: PMC7058675 DOI: 10.1007/s00018-019-03421-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/04/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has explained some of the 'missing heritability' of age-related macular degeneration (AMD). The epigenome also provides a substantial contribution to the organisation of the functional retina. There is emerging evidence of specific epigenetic mechanisms associated with AMD. This 'AMD epigenome' may offer the chance to develop novel AMD treatments.
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Affiliation(s)
- M Gemenetzi
- NIHR Biomedical Research Centre At Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, 162 City Road, London, EC1V 2PD, UK
| | - A J Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University Hospital Southampton, University of Southampton, South Lab and Path Block, Mailpoint 806, Level D, Southampton, SO16 6YD, UK.
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10
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Advances in epigenetics link genetics to the environment and disease. Nature 2019; 571:489-499. [DOI: 10.1038/s41586-019-1411-0] [Citation(s) in RCA: 566] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022]
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11
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Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nat Commun 2019; 10:34. [PMID: 30604769 PMCID: PMC6318327 DOI: 10.1038/s41467-018-08006-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 01/18/2023] Open
Abstract
The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs are increasingly recognized for their important biological functions, they are a potential danger to genomic stability and are carefully regulated by the epigenetic system. However, the full complexity of this regulatory system is not understood. Here, using mouse embryonic stem cells, we show that TEs are suppressed by heterochromatic marks like H3K9me3, and are also labelled by all major types of chromatin modification in complex patterns, including bivalent activatory and repressive marks. We identified 29 epigenetic modifiers that significantly deregulated at least one type of TE. The loss of Setdb1, Ncor2, Rnf2, Kat5, Prmt5, Uhrf1, and Rrp8 caused widespread changes in TE expression and chromatin accessibility. These effects were context-specific, with different chromatin modifiers regulating the expression and chromatin accessibility of specific subsets of TEs. Our work reveals the complex patterns of epigenetic regulation of TEs. Transposable elements (TEs) fulfill essential but poorly understood roles in genome organization and gene expression control. Here the authors show that the regulation of TEs occurs through overlapping epigenetic mechanisms that control the expression and chromatin signatures at TEs.
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12
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Guio L, González J. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans. Methods Mol Biol 2019; 1910:505-530. [PMID: 31278675 DOI: 10.1007/978-1-4939-9074-0_16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.
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Affiliation(s)
- Lain Guio
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
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13
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The cell cycle regulatory DREAM complex is disrupted by high expression of oncogenic B-Myb. Oncogene 2018; 38:1080-1092. [PMID: 30206359 PMCID: PMC6377300 DOI: 10.1038/s41388-018-0490-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022]
Abstract
Overexpression of the oncogene MYBL2 (B-Myb) is associated with increased cell proliferation and serves as marker of poor prognosis in cancer. However, the mechanism by which B-Myb alters the cell cycle is not fully understood. In proliferating cells, B-Myb interacts with the MuvB core complex including LIN9, LIN37, LIN52, RBBP4, and LIN54, forming the MMB (Myb-MuvB) complex, and promotes transcription of genes required for mitosis. Alternatively, the MuvB core interacts with Rb-like protein p130 and E2F4-DP1 to form the DREAM complex that mediates global repression of cell cycle genes in G0/G1, including a subset of MMB target genes. Here, we show that overexpression of B-Myb disrupts the DREAM complex in human cells, and this activity depends on the intact MuvB-binding domain in B-Myb. Furthermore, we found that B-Myb regulates the protein expression levels of the MuvB core subunit LIN52, a key adaptor for assembly of both the DREAM and MMB complexes, by a mechanism that requires S28 phosphorylation site in LIN52. Given that high expression of B-Myb correlates with global loss of repression of DREAM target genes in breast and ovarian cancer, our findings offer mechanistic insights for aggressiveness of cancers with MYBL2 amplification, and establish the rationale for targeting B-Myb to restore cell cycle control.
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14
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Vitas M, Dobovišek A. In the Beginning was a Mutualism - On the Origin of Translation. ORIGINS LIFE EVOL B 2018; 48:223-243. [PMID: 29713988 DOI: 10.1007/s11084-018-9557-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/23/2018] [Indexed: 12/28/2022]
Abstract
The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.
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Affiliation(s)
- Marko Vitas
- , Laze pri Borovnici 38, Borovnica, Slovenia.
| | - Andrej Dobovišek
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia
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Laubach ZM, Perng W, Dolinoy DC, Faulk CD, Holekamp KE, Getty T. Epigenetics and the maintenance of developmental plasticity: extending the signalling theory framework. Biol Rev Camb Philos Soc 2018; 93:1323-1338. [PMID: 29356358 DOI: 10.1111/brv.12396] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022]
Abstract
Developmental plasticity, a phenomenon of importance in both evolutionary biology and human studies of the developmental origins of health and disease (DOHaD), enables organisms to respond to their environment based on previous experience without changes to the underlying nucleotide sequence. Although such phenotypic responses should theoretically improve an organism's fitness and performance in its future environment, this is not always the case. Herein, we first discuss epigenetics as an adaptive mechanism of developmental plasticity and use signaling theory to provide an evolutionary context for DOHaD phenomena within a generation. Next, we utilize signalling theory to identify determinants of adaptive developmental plasticity, detect sources of random variability - also known as process errors that affect maintenance of an epigenetic signal (DNA methylation) over time, and discuss implications of these errors for an organism's health and fitness. Finally, we apply life-course epidemiology conceptual models to inform study design and analytical strategies that are capable of parsing out the potential effects of process errors in the relationships among an organism's early environment, DNA methylation, and phenotype in a future environment. Ultimately, we hope to foster cross-talk and interdisciplinary collaboration between evolutionary biology and DOHaD epidemiology, which have historically remained separate despite a shared interest in developmental plasticity.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
| | - Wei Perng
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A.,Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A
| | - Dana C Dolinoy
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A.,Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A
| | - Christopher D Faulk
- Department of Animal Sciences, University of Minnesota, 495B AnSc/VetMed, 1988 Fitch Avenue, St. Paul, MN, 55108, U.S.A
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
| | - Thomas Getty
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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17
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Abstract
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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