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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 01/05/2024] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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2
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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Complexification of eukaryote phenotype: Adaptive immuno-cognitive systems as unique Gödelian block chain distributed ledger. Biosystems 2022; 220:104718. [PMID: 35803502 DOI: 10.1016/j.biosystems.2022.104718] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 12/26/2022]
Abstract
The digitization of inheritable information in the genome has been called the 'algorithmic take-over of biology'. The McClintock discovery that viral software based transposable elements that conduct cut-paste (transposon) and copy-paste (retrotransposon) operations are needed for genomic evolvability underscores the truism that only software can change software and also that viral hacking by internal and external bio-malware is the Achilles heel of genomic digital systems. There was a paradigm shift in genomic information processing with the Adaptive Immune System (AIS) 500 mya followed by the Mirror Neuron System (MNS), latterly mostly in primate brains, which reaches its apogee in human social cognition. The AIS and MNS involve distinctive Gödelian features of self-reference (Self-Ref) and offline virtual self-representation (Self-Rep) for complex self-other interaction with prodigious open-ended capacity for anticipative malware detection and novelty production within a unique blockchain distributed ledger (BCDL). The role of self-referential information processing, often considered to be central to the sentient self with origins in the immune system 'Thymic self', is shown to be part of the Gödel logic behind a generator-selector framework at a molecular level, which exerts stringent selection criteria to maintain genomic BCDL. The latter manifests digital and decentralized record keeping where no internal or external bio-malware can compromise the immutability of the life's building blocks and no novel blocks can be added that is not consistent with extant blocks. This is demonstrated with regard to somatic hypermutation with novel anti-body production in the face of external non-self antigen attacks.
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Sultan SE, Moczek AP, Walsh D. Bridging the explanatory gaps: What can we learn from a biological agency perspective? Bioessays 2021; 44:e2100185. [PMID: 34747061 DOI: 10.1002/bies.202100185] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022]
Abstract
We begin this article by delineating the explanatory gaps left by prevailing gene-focused approaches in our understanding of phenotype determination, inheritance, and the origin of novel traits. We aim not to diminish the value of these approaches but to highlight where their implementation, despite best efforts, has encountered persistent limitations. We then discuss how each of these explanatory gaps can be addressed by expanding research foci to take into account biological agency-the capacity of living systems at various levels to participate in their own development, maintenance, and function by regulating their structures and activities in response to conditions they encounter. Here we aim to define formally what agency and agents are and-just as importantly-what they are not, emphasizing that agency is an empirical property connoting neither intention nor consciousness. Lastly, we discuss how incorporating agency helps to bridge explanatory gaps left by conventional approaches, highlight scientific fields in which implicit agency approaches are already proving valuable, and assess the opportunities and challenges of more systematically incorporating biological agency into research programs.
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Affiliation(s)
- Sonia E Sultan
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Denis Walsh
- Department of Philosophy, Institute for the History and Philosophy of Science and Technology, Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Posner R, Toker IA, Antonova O, Star E, Anava S, Azmon E, Hendricks M, Bracha S, Gingold H, Rechavi O. Neuronal Small RNAs Control Behavior Transgenerationally. Cell 2019; 177:1814-1826.e15. [PMID: 31178120 PMCID: PMC6579485 DOI: 10.1016/j.cell.2019.04.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/18/2019] [Accepted: 04/13/2019] [Indexed: 12/21/2022]
Abstract
It is unknown whether the activity of the nervous system can be inherited. In Caenorhabditis elegans nematodes, parental responses can transmit heritable small RNAs that regulate gene expression transgenerationally. In this study, we show that a neuronal process can impact the next generations. Neurons-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous small interfering RNAs (siRNAs) and germline gene expression for multiple generations. Further, the production of small RNAs in neurons controls the chemotaxis behavior of the progeny for at least three generations via the germline Argonaute HRDE-1. Among the targets of these small RNAs, we identified the conserved gene saeg-2, which is transgenerationally downregulated in the germline. Silencing of saeg-2 following neuronal small RNA biogenesis is required for chemotaxis under stress. Thus, we propose a small-RNA-based mechanism for communication of neuronal processes transgenerationally. C. elegans neuronal small RNAs are characterized by RNA sequencing RDE-4-dependent neuronal endogenous small RNAs communicate with the germline Germline HRDE-1 mediates transgenerational regulation by neuronal small RNAs Neuronal small RNAs regulate germline genes to control behavior transgenerationally
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Affiliation(s)
- Rachel Posner
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itai Antoine Toker
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Olga Antonova
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ekaterina Star
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sarit Anava
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eran Azmon
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michael Hendricks
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Shahar Bracha
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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Steele EJ, Al-Mufti S, Augustyn KA, Chandrajith R, Coghlan JP, Coulson SG, Ghosh S, Gillman M, Gorczynski RM, Klyce B, Louis G, Mahanama K, Oliver KR, Padron J, Qu J, Schuster JA, Smith WE, Snyder DP, Steele JA, Stewart BJ, Temple R, Tokoro G, Tout CA, Unzicker A, Wainwright M, Wallis J, Wallis DH, Wallis MK, Wetherall J, Wickramasinghe DT, Wickramasinghe JT, Wickramasinghe NC, Liu Y. Cause of Cambrian Explosion - Terrestrial or Cosmic? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 136:3-23. [PMID: 29544820 DOI: 10.1016/j.pbiomolbio.2018.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion - life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.
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Affiliation(s)
- Edward J Steele
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka.
| | - Shirwan Al-Mufti
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Kenneth A Augustyn
- Center for the Physics of Living Organisms, Department of Physics, Michigan Technological University, Michigan, United States
| | | | - John P Coghlan
- University of Melbourne, Office of the Dean, Faculty Medicine, Dentistry and Health Sciences, 3rd Level, Alan Gilbert Building, Australia
| | - S G Coulson
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Sudipto Ghosh
- Metallurgical & Materials Engineering IIT, Kanpur, India
| | - Mark Gillman
- South African Brain Research Institute, 6 Campbell Street, Waverly, Johannesburg, South Africa
| | - Reginald M Gorczynski
- University Toronto Health Network, Toronto General Hospital, University of Toronto, Canada
| | - Brig Klyce
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Godfrey Louis
- Department of Physics, Cochin University of Science and Technology Cochin, India
| | | | - Keith R Oliver
- School of Veterinary and Life Sciences Murdoch University, Perth, WA, Australia
| | - Julio Padron
- Studio Eutropi, Clinical Pathology and Nutrition, Via Pompei 46, Ardea, 00040, Rome, Italy
| | - Jiangwen Qu
- Department of Infectious Disease Control, Tianjin Center for Disease Control and Prevention, China
| | - John A Schuster
- School of History and Philosophy of Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - W E Smith
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Duane P Snyder
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Julian A Steele
- Centre for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Brent J Stewart
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
| | - Robert Temple
- The History of Chinese Culture Foundation, Conway Hall, London, UK
| | - Gensuke Tokoro
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Christopher A Tout
- Institute of Astronomy, The Observatories, Madingley Road, Cambridge, CB3 0HA, UK
| | | | - Milton Wainwright
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka
| | - Jamie Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Daryl H Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Max K Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - John Wetherall
- School of Biomedical Sciences, Perth, Curtin University, WA, Australia
| | - D T Wickramasinghe
- College of Physical and Mathematical Sciences, Australian National University, Canberra, Australia
| | | | - N Chandra Wickramasinghe
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Abstract
Stochasticity is harnessed by organisms to generate functionality. Randomness does not, therefore, necessarily imply lack of function or 'blind chance' at higher levels. In this respect, biology must resemble physics in generating order from disorder. This fact is contrary to Schrödinger's idea of biology generating phenotypic order from molecular-level order, which inspired the central dogma of molecular biology. The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of transcription factors and various epigenetic and reorganization mechanisms. These processes can occur in response to environmental stress, so that the genome becomes 'a highly sensitive organ of the cell' (McClintock). Organisms have evolved to be able to cope with many variations at the molecular level. Organisms also make use of physical processes in evolution and development when it is possible to arrive at functional development without the necessity to store all information in DNA sequences. This view of development and evolution differs radically from that of neo-Darwinism with its emphasis on blind chance as the origin of variation. Blind chance is necessary, but the origin of functional variation is not at the molecular level. These observations derive from and reinforce the principle of biological relativity, which holds that there is no privileged level of causation. They also have important implications for medical science.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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8
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Villarreal LP. Persistent virus and addiction modules: an engine of symbiosis. Curr Opin Microbiol 2016; 31:70-79. [PMID: 27039268 DOI: 10.1016/j.mib.2016.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 12/14/2022]
Abstract
The giant DNA viruses are highly prevalent and have a particular affinity for the lytic infection of unicellular eukaryotic host. The giant viruses can also be infected by inhibitory virophage which can provide lysis protection to their host. The combined protective and destructive action of such viruses can define a general model (PD) of virus-mediated host survival. Here, I present a general model for role such viruses play in the evolution of host symbiosis. By considering how virus mixtures can participate in addiction modules, I provide a functional explanation for persistence of virus derived genetic 'junk' in their host genomic habitats.
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Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, University of California, Irvine, Irvine, CA 926197, USA.
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9
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Abstract
PURPOSE OF REVIEW The review aims to provide a summary of recent developments in the study of gene expression in the aging human brain. RECENT FINDINGS Profiling differentially expressed genes or 'transcripts' in the human brain over the course of normal aging has provided valuable insights into the biological pathways that appear activated or suppressed in late life. Genes mediating neuroinflammation and immune system activation in particular, show significant age-related upregulation creating a state of vulnerability to neurodegenerative and neuropsychiatric disease in the aging brain. Cellular ionic dyshomeostasis and age-related decline in a host of molecular influences on synaptic efficacy may underlie neurocognitive decline in later life. Critically, these investigations have also shed light on the mobilization of protective genetic responses within the aging human brain that help determine health and disease trajectories in older age. There is growing interest in the study of pre and posttranscriptional regulators of gene expression, and the role of noncoding RNAs in particular, as mediators of the phenotypic diversity that characterizes human brain aging. SUMMARY Gene expression studies in healthy brain aging offer an opportunity to unravel the intricately regulated cellular underpinnings of neurocognitive aging as well as disease risk and resiliency in late life. In doing so, new avenues for early intervention in age-related neurodegenerative disease could be investigated with potentially significant implications for the development of disease-modifying therapies.
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Steele EJ, Lloyd SS. Soma-to-germline feedback is implied by the extreme polymorphism at IGHV relative to MHC: The manifest polymorphism of the MHC appears greatly exceeded at Immunoglobulin loci, suggesting antigen-selected somatic V mutants penetrate Weismann's Barrier. Bioessays 2015; 37:557-69. [PMID: 25810320 DOI: 10.1002/bies.201400213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/15/2015] [Accepted: 02/24/2015] [Indexed: 01/22/2023]
Abstract
Soma-to-germline feedback is forbidden under the neo-Darwinian paradigm. Nevertheless, there is a growing realization it occurs frequently in immunoglobulin (Ig) variable (V) region genes. This is a surprising development. It arises from a most unlikely source in light of the exposure of co-author EJS to the haplotype data of RL Dawkins and others on the polymorphism of the Major Histocompatibility Complex, which is generally assumed to be the most polymorphic region in the genome (spanning ∼4 Mb). The comparison between the magnitude of MHC polymorphism with estimates for the human heavy chain immunoglobulin V locus (spanning ∼1 Mb), suggests IGHV could be many orders of magnitude more polymorphic than the MHC. This conclusion needs airing in the literature as it implies generational churn and soma-to-germline gene feedback. Pedigree-based experimental strategies to resolve the IGHV issue are outlined.
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Affiliation(s)
- Edward J Steele
- C.Y. O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
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12
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Anava S, Posner R, Rechavi O. The soft genome. WORM 2015; 3:e989798. [PMID: 26430554 DOI: 10.4161/21624054.2014.989798] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022]
Abstract
Caenorhabditis elegans (C. elegans) nematodes transmit small RNAs across generations, a process that enables transgenerational regulation of genes. In contrast to changes to the DNA sequence, transgenerational transmission of small RNA-mediated responses is reversible, and thus enables "soft" or "flexible" inheritance of acquired characteristics. Until very recently only introduction of foreign genetic material (viruses, transposons, transgenes) was shown to directly lead to inheritance of small RNAs. New discoveries however, demonstrate that starvation also triggers inheritance of endogenous small RNAs in C.elegans. Multiple generations of worms inherit starvation-responsive endogenous small RNAs, and starvation also results in heritable extension of the progeny's lifespan. In this Commentary paper we explore the intriguing possibility that large parts of the genome and many additional traits are similarly subjected to heritable small RNA-mediated regulation, and focus on the potential influence of transgenerational RNAi on the worm's physiology. While the universal relevance of this mechanism remains to be discovered, we will examine how the discoveries made in worms already challenge long held dogmas in genetics and evolution.
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Affiliation(s)
- Sarit Anava
- Department of Neurobiology; Wise Faculty of Life Sciences & Sagol School of Neuroscience; Tel Aviv University ; Tel Aviv, Israel
| | - Rachel Posner
- Department of Neurobiology; Wise Faculty of Life Sciences & Sagol School of Neuroscience; Tel Aviv University ; Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology; Wise Faculty of Life Sciences & Sagol School of Neuroscience; Tel Aviv University ; Tel Aviv, Israel
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13
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Abstract
Poised at a critical turning point in the history of genetics, recent work (e.g. in genomics, epigenetics, genomic plasticity) obliges us to critically reexamine many of our most basic concepts. For example, I argue that genomic research supports a radical transformation in our understanding of the genome--a shift from an earlier conception of that entity as an effectively static collection of active genes to that of a dynamic and reactive system dedicated to the context specific regulation of protein-coding sequences.
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Affiliation(s)
- Evelyn Fox Keller
- MIT, Program in Science, Technology, and Society, Cambridge, MA 02139, USA
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14
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Noble D, Jablonka E, Joyner MJ, Müller GB, Omholt SW. Evolution evolves: physiology returns to centre stage. J Physiol 2015; 592:2237-44. [PMID: 24882808 DOI: 10.1113/jphysiol.2014.273151] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Denis Noble
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, UK
| | - Eva Jablonka
- Tel Aviv University, Cohn Institute for the History and Philosophy of Science and Ideas, Ramat Aviv, Israel
| | | | - Gerd B Müller
- University of Vienna, Department of Theoretical Biology, Vienna, Austria
| | - Stig W Omholt
- Norwegian University of Science and Technology, Faculty of Medicine, Trondheim, Norway
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15
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Sharma A. Systems genomics analysis centered on epigenetic inheritance supports development of a unified theory of biology. J Exp Biol 2015; 218:3368-73. [DOI: 10.1242/jeb.125922] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/20/2015] [Indexed: 12/18/2022]
Abstract
New discoveries are increasingly demanding integration of epigenetics, molecular biology, genomic networks, and physiology with evolution. This article provides a proof of concept for evolutionary transgenerational systems biology, proposed recently in the context of epigenetic inheritance in mammals. Gene set enrichment analysis of available genome level mammalian data presented here seems consistent with the concept that (1) heritable information about environmental effects in somatic cells is communicated to the germline by circulating microRNAs (miRNAs) or other RNAs released in physiological fluids, (2) epigenetic factors including miRNA-like small RNAs, DNA methylation and histone modifications are propagated across generations via gene networks, and (3) inherited epigenetic variations in the form of methylated cytosines are fixed in the population as thymines in evolutionary time course. The analysis supports integration of physiology and epigenetics with inheritance and evolution. This may catalyze efforts to develop a unified theory of biology.
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Affiliation(s)
- Abhay Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, New Delhi 110025, India
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16
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Guennewig B, Cooper AA. The Central Role of Noncoding RNA in the Brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:153-94. [DOI: 10.1016/b978-0-12-801105-8.00007-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Brien FD, Cloete SWP, Fogarty NM, Greeff JC, Hebart ML, Hiendleder S, Edwards JEH, Kelly JM, Kind KL, Kleemann DO, Plush KL, Miller DR. A review of the genetic and epigenetic factors affecting lamb survival. ANIMAL PRODUCTION SCIENCE 2014. [DOI: 10.1071/an13140] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Poor lamb survival pre-weaning is a major source of reproductive inefficiency in Australian sheep flocks. While nutrition and management options have been extensively researched and promoted to improve lamb survival, the present review focuses on the prospects for obtaining genetic gain and helps identify selection strategies for boosting such gains to improve overall reproductive efficiency in the Australian sheep industry. Estimated heritability for lamb survival using linear model analysis is low, although use of threshold models suggests that heritability could be higher, which, if true, could help explain the substantial genetic gains obtained in long-term selection experiments. Epigenetic mechanisms may hinder selection and quantitative trait-loci identification through confounding and/or masking genetic variances and co-variances. With sufficient information, these effects could be considered in genetic evaluations by identifying those components that are amenable to selection. Regarding indirect selection, finding effective criteria for improving lamb survival has proved elusive. Most measures of maternal behaviour, temperament and lambing difficulty researched are poorly correlated genetically with lamb survival. Of lamb behaviours and thermo-genic indicators studied, latency to bleat following handling by humans is moderately genetically correlated with lamb survival, as is neonatal rectal temperature. Industry application remains to be adequately explored for the more promising of these measures. Finally, in lieu of direct selection for lamb survival, there is merit in selecting for multiple-rearing ability or its equivalent, possibly with additional selection criteria for lamb survival and reproductive efficiency.
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Noble D. Systems biology and reproduction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:355. [PMID: 24314295 DOI: 10.1016/j.pbiomolbio.2013.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Rechavi O. Guest list or black list: heritable small RNAs as immunogenic memories. Trends Cell Biol 2013; 24:212-20. [PMID: 24231398 DOI: 10.1016/j.tcb.2013.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/10/2013] [Accepted: 10/11/2013] [Indexed: 11/24/2022]
Abstract
Small RNA-mediated gene silencing plays a pivotal role in genome immunity by recognizing and eliminating viruses and transposons that may otherwise colonize the genome. However, individual genomic parasites are highly diverse and employ multiple immune-evasion techniques, making this silencing challenging. Here I review a new theory proposing that the integrity of the germline is maintained by transgenerationally transmitted RNA 'memories' that record ancestral gene expression patterns and delineate 'self' from 'foreign' sequences. To maintain such recollection, two tactics are employed in parallel: 'black listing' of invading nucleic acids and 'guest listing' of endogenous genes. Studies in several organisms have shown that this memorization is used by the next generation of small RNAs to act as 'inherited vaccines' that attack invading elements or as 'inherited licenses' that permit the transcription of autogenous sequences.
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Affiliation(s)
- Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 69978; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel 69978.
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Shang L, Gardner DP, Xu W, Cannone JJ, Miranker DP, Ozer S, Gutell RR. Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 4:S13. [PMID: 24565058 PMCID: PMC3854672 DOI: 10.1186/1752-0509-7-s4-s13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data. Methods Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. Multiple dimensions of cross-indexed information are contained within the relational database - rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. The first program, CRWAlign-1 creates a phylogenetic-based sequence profile for each column in the alignment. The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. Both programs utilize their profiles to align new sequences into the template alignment. Results The accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. We have compared our programs with a total of eight alternative alignment methods on different sets of 16S rRNA alignments with sequence percent identities ranging from 50% to 100%. Both CRWAlign programs were superior to these other programs in accuracy and speed. Conclusions Both CRWAlign programs can be used to align the very extensive amount of RNA sequencing that is generated due to the rapid next-generation sequencing technology. This latter technology is augmenting the new paradigm that RNA is intimately implicated in a significant number of functions within the cell. In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences.
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The intertwining of transposable elements and non-coding RNAs. Int J Mol Sci 2013; 14:13307-28. [PMID: 23803660 PMCID: PMC3742188 DOI: 10.3390/ijms140713307] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/05/2013] [Accepted: 06/05/2013] [Indexed: 12/15/2022] Open
Abstract
Growing evidence shows a close association of transposable elements (TE) with non-coding RNAs (ncRNA), and a significant number of small ncRNAs originate from TEs. Further, ncRNAs linked with TE sequences participate in a wide-range of regulatory functions. Alu elements in particular are critical players in gene regulation and molecular pathways. Alu sequences embedded in both long non-coding RNAs (lncRNA) and mRNAs form the basis of targeted mRNA decay via short imperfect base-pairing. Imperfect pairing is prominent in most ncRNA/target RNA interactions and found throughout all biological kingdoms. The piRNA-Piwi complex is multifunctional, but plays a major role in protection against invasion by transposons. This is an RNA-based genetic immune system similar to the one found in prokaryotes, the CRISPR system. Thousands of long intergenic non-coding RNAs (lincRNAs) are associated with endogenous retrovirus LTR transposable elements in human cells. These TEs can provide regulatory signals for lincRNA genes. A surprisingly large number of long circular ncRNAs have been discovered in human fibroblasts. These serve as "sponges" for miRNAs. Alu sequences, encoded in introns that flank exons are proposed to participate in RNA circularization via Alu/Alu base-pairing. Diseases are increasingly found to have a TE/ncRNA etiology. A single point mutation in a SINE/Alu sequence in a human long non-coding RNA leads to brainstem atrophy and death. On the other hand, genomic clusters of repeat sequences as well as lncRNAs function in epigenetic regulation. Some clusters are unstable, which can lead to formation of diseases such as facioscapulohumeral muscular dystrophy. The future may hold more surprises regarding diseases associated with ncRNAs andTEs.
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Lelandais-Brière C, Sorin C, Crespi M, Hartmann C. [Non-coding RNAs involved in plant responses to environmental constraints]. Biol Aujourdhui 2013; 206:313-22. [PMID: 23419258 DOI: 10.1051/jbio/2012032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Indexed: 12/20/2022]
Abstract
In recent years, in addition to mRNAs, the non-protein-coding RNAs (or ncRNAs) have emerged as a major part of the eukaryotic transcriptome. New genomic approaches allowed the discovery of many novel long and small ncRNAs that may be linked to the generation of evolutionary complexity in multicellular organisms. Many long ncRNAs are regulated by abiotic stresses although only very few long ncRNAs have been functionally analyzed. On the other hand, small RNAs act in the regulation of gene expression at transcriptional or post-transcriptional level and several among them have been linked to abiotic stress responses. Here we describe various ncRNAs associated with environmental stress responses such as to salt, cold or nutrient deprivation. The understanding of these RNA networks may reveal novel mechanisms involved in plant adaptation to changing environmental conditions.
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Affiliation(s)
- Christine Lelandais-Brière
- Université Paris-Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France - Institut des Sciences du Végétal ISV, CNRS, UPR2355, 91198 Gif-sur-Yvette Cedex, France
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