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Lakhotia SC. C-value paradox: Genesis in misconception that natural selection follows anthropocentric parameters of 'economy' and 'optimum'. BBA ADVANCES 2023; 4:100107. [PMID: 37868661 PMCID: PMC10587719 DOI: 10.1016/j.bbadva.2023.100107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
C-value paradox refers to the lack of correlation between biological complexity and the intuitively expected protein-coding genomic information or DNA content. Here I discuss five questions about this paradox: i) Do biologically complex organisms carry more protein-coding genes? ii) Does variable accumulation of selfish/ junk/ parasitic DNA underlie the c-value paradox? iii) Can nucleoskeletal or nucleotypic function of DNA explain the enigma of orders of magnitude high levels of DNA in some 'lower' taxa or in taxonomically related species? iv) Can the newly understood noncoding but functional DNA explain the c-value paradox? and, v) Does natural selection uniformly apply the anthropocentric parameters for 'optimum' and 'economy'? Answers to Q.1-5 are largely negative. Biology presents numerous 'anomalous' examples where the same end function/ phenotype is attained in different organisms through astoundingly diverse ways that appear 'illogical' in our perceptions. Such evolutionary oddities exist because natural selection, unlike a designer, exploits random and stochastic events to modulate the existing system. Consequently, persistence of the new-found 'solution/s' often appear bizarre, uneconomic, and therefore, paradoxical to human logic. The unexpectedly high c-values in diverse organisms are irreversible evolutionary accidents that persisted, and the additional DNA often got repurposed over the evolutionary time scale. Therefore, the c-value paradox is a redundant issue. Future integrative biological studies should address evolutionary mechanisms and processes underlying sporadic DNA expansions/ contractions, and how the newly acquired DNA content has been repurposed in diverse groups.
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Affiliation(s)
- Subhash C. Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Alfimova MV, Kondratiev NV, Golimbet VE. Results and promises of genetics of cognitive impairment in schizophrenia: epigenetic approaches. Zh Nevrol Psikhiatr Im S S Korsakova 2017. [DOI: 10.17116/jnevro201711721130-135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Glavey SV, Manier S, Sacco A, Salem K, Kawano Y, Bouyssou J, Ghobrial IM, Roccaro AM. Epigenetics in Multiple Myeloma. Cancer Treat Res 2016; 169:35-49. [PMID: 27696257 DOI: 10.1007/978-3-319-40320-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Multiple myeloma is characterized by clonal proliferation of plasma cells within the bone marrow resulting in anemia, lytic bone lesions, hypercalcemia, and renal impairment. Despite advanced in our understanding of this complex disease in recent years, it is still considered an incurable malignancy. This is, in part, due to the highly heterogenous genomic and phenotypic nature of the disease, which is to date incompletely understood. It is clear that a deeper level of knowledge of the biological events underlying the development of these diseases is needed to identify new targets and generate effective novel therapies. MicroRNAs (miRNAs), which are single strand, 20-nucleotide, noncoding RNA's, are key regulators of gene expression and have been reported to exert transcriptional control in multiple myeloma. miRNAs are now recognized to play a role in many key areas such as cellular proliferation, differentiation, apoptosis and stress response. Substantial advances have been made in recent years in terms of our understanding of the biological role of miRNAs in a diverse range of hematological and solid malignancues, In multiple myeloma these advances have yielded new information of prognostic and diagnostic relevance which have helped to shed light on epigenetic regulation in this disease.
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Affiliation(s)
- Siobhan V Glavey
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Salomon Manier
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Antonio Sacco
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karma Salem
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yawara Kawano
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Juliette Bouyssou
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Irene M Ghobrial
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aldo M Roccaro
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Hematology, CREA Laboratory, ASST-Spedali Civili di Brescia, Brescia, BS, Italy.
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Page A, Mann DA, Mann J. The mechanisms of HSC activation and epigenetic regulation of HSCs phenotypes. CURRENT PATHOBIOLOGY REPORTS 2014; 2:163-170. [PMID: 27413631 DOI: 10.1007/s40139-014-0052-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Epigenetics is a dynamically expanding field of science entailing numerous regulatory mechanisms controlling changes of gene expression in response to environmental factors. Over the recent years there has been a great interest in epigenetic marks as a potential diagnostic and prognostic tool or future target for treatment of various human diseases. There is an increasing body of published research to suggest that epigenetic events regulate progression of chronic liver disease. Experimental manipulation of epigenetic signatures such as DNA methylation, histone acetylation / methylation and the activities of proteins that either annotate or interpret these epigenetic marks can have profound effects on the activation and phenotype of HSC, key cells responsible for onset and progression of liver fibrosis. This review presents recent advances in epigenetic alterations, which could provide mechanistic insight into the pathogenesis of chronic liver disease and provide novel clinical applications.
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Affiliation(s)
- Agata Page
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4 Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Derek A Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4 Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jelena Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4 Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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Affiliation(s)
- J. Rich
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
| | - V. V. Ogryzko
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
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Zeybel M, Hardy T, Wong YK, Mathers JC, Fox CR, Gackowska A, Oakley F, Burt AD, Wilson CL, Anstee QM, Barter MJ, Masson S, Elsharkawy AM, Mann DA, Mann J. Multigenerational epigenetic adaptation of the hepatic wound-healing response. Nat Med 2012; 18:1369-77. [PMID: 22941276 PMCID: PMC3489975 DOI: 10.1038/nm.2893] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 07/02/2012] [Indexed: 02/06/2023]
Abstract
We investigated whether ancestral liver damage leads to heritable reprogramming of hepatic wound healing in male rats. We found that a history of liver damage corresponds with transmission of an epigenetic suppressive adaptation of the fibrogenic component of wound healing to the male F1 and F2 generations. Underlying this adaptation was less generation of liver myofibroblasts, higher hepatic expression of the antifibrogenic factor peroxisome proliferator-activated receptor γ (PPAR-γ) and lower expression of the profibrogenic factor transforming growth factor β1 (TGF-β1) compared to rats without this adaptation. Remodeling of DNA methylation and histone acetylation underpinned these alterations in gene expression. Sperm from rats with liver fibrosis were enriched for the histone variant H2A.Z and trimethylation of histone H3 at Lys27 (H3K27me3) at PPAR-γ chromatin. These modifications to the sperm chromatin were transmittable by adaptive serum transfer from fibrotic rats to naive rats and similar modifications were induced in mesenchymal stem cells exposed to conditioned media from cultured rat or human myofibroblasts. Thus, it is probable that a myofibroblast-secreted soluble factor stimulates heritable epigenetic signatures in sperm so that the resulting offspring better adapt to future fibrogenic hepatic insults. Adding possible relevance to humans, we found that people with mild liver fibrosis have hypomethylation of the PPARG promoter compared to others with severe fibrosis.
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Affiliation(s)
- Müjdat Zeybel
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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Perugorria MJ, Wilson CL, Zeybel M, Walsh M, Amin S, Robinson S, White SA, Burt AD, Oakley F, Tsukamoto H, Mann DA, Mann J. Histone methyltransferase ASH1 orchestrates fibrogenic gene transcription during myofibroblast transdifferentiation. Hepatology 2012; 56:1129-39. [PMID: 22488473 PMCID: PMC3430805 DOI: 10.1002/hep.25754] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 03/24/2012] [Indexed: 12/12/2022]
Abstract
UNLABELLED Transdifferentiation of hepatic stellate cells (HSCs) to a myofibroblast-like phenotype is the pivotal event in liver fibrosis. The dramatic change in phenotype associated with transdifferentiation is underpinned by a global change in gene expression. Orchestrated changes in gene expression take place at the level of chromatin packaging which is regulated by enzymatic activity of epigenetic regulators that in turn affect histone modifications. Using expression profiling of epigenetic regulators in quiescent and activated primary HSCs we found a number of histone methyltransferases including MLL1, MLL5, Set1 and ASH1 to be highly up-regulated during transdifferentiation of HSCs. All of these histone methyltransferases regulate methylation of lysine 4 of histone H3, which is a signature of actively transcribed genes. We therefore postulated that one or more of these enzymes may be involved in positively influencing expression of profibrogenic genes. CONCLUSION We find that ASH1 directly binds to the regulatory regions of alpha smooth muscle actin (αSMA), collagen I, tissue inhibitor of metalloproteinase-1 (TIMP1) and transforming growth factor beta1 (TGFβ1) in activated HSCs while depletion of ASH1 caused broad suppression of fibrogenic gene expression. We also discovered that MeCP2 positively regulates ASH1 expression and therefore identify ASH1 as a key transcriptional activator component of the MeCP2 epigenetic relay pathway that orchestrates coordinated induction of multiple profibrogenic genes.
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Affiliation(s)
- Maria Jesus Perugorria
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Caroline L Wilson
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Mujdat Zeybel
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Meagan Walsh
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Shilu Amin
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Stuart Robinson
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Steven A White
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Alastair D Burt
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Fiona Oakley
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Hidekazu Tsukamoto
- Southern California Research Center for ALPD and Cirrhosis, Keck School of Medicine of the University of Southern California, Department of Veterans Affairs Greater Los Angeles Healthcare SystemLos Angeles, CA, USA
| | - Derek A Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Jelena Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle UniversityNewcastle upon Tyne, UK
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Crombach A, Hogeweg P. Is RNA-dependent RNA polymerase essential for transposon control? BMC SYSTEMS BIOLOGY 2011; 5:104. [PMID: 21714914 PMCID: PMC3155503 DOI: 10.1186/1752-0509-5-104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/29/2011] [Indexed: 11/29/2022]
Abstract
Background Eukaryotes use RNA interference and RNA-based epigenetic regulation to control transposon activity. In the standard pathways of RNA-based transcriptional and post-transcriptional silencing the protein complex RNA-dependent RNA polymerase (RdRP) plays a crucial role. However, alternative pathways that bypass RdRP have recently been described. Hence two important questions are: is RdRP truly a necessary component for transposon control, and are the alternative RNA-based strategies also capable of controlling transposable elements? Results We have studied the interplay between host RNAi pathways and transposons using mathematical models. We show that the canonical RdRP-based model controls transposons tightly, mainly via the feedback of cytoplasmic small RNA amplification. Next, we consider two variants lacking RdRP and instead employing antisense transcription of transposons. We show that transposon activity is also controlled by the alternative pathways, although cytoplasmic small RNA amplification is absent. Instead, control occurs in the nucleus, through a feedback in the epigenetic regulation. Conclusions Concluding, our models show that the control of transposon activity can be achieved by alternative pathways that lack RdRP and act through different feedback mechanisms. Thus, although RdRP activity is ubiquitous in eukaryotes, it need not be a general requirement for transposon control.
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Affiliation(s)
- Anton Crombach
- Theoretical Biology and Bioinformatics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Lipovich L, Johnson R, Lin CY. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:597-615. [PMID: 20951849 DOI: 10.1016/j.bbagrm.2010.10.001] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 08/13/2010] [Accepted: 10/06/2010] [Indexed: 12/19/2022]
Abstract
The central dogma of molecular biology relegates RNAs to the role of "messengers" of genetic information, with proteins as the end products that perform key roles as regulators and effectors of biological processes. Notable exceptions include non-protein-coding RNAs, which function as adaptors (tRNAs) and ribosomal components (rRNAs) during translation, as well as in splicing (snRNAs) and RNA maturation including editing (snoRNAs). Genome and transcriptome projects have revealed, however, a significant number, rivaling the protein-coding transcripts, of non-protein-coding RNAs not related to these previously characterized transcript classes. Non-protein-coding RNA research has primarily focused on microRNAs, a small subclass of non-protein-coding RNAs, and their regulatory roles in gene expression, and these findings have been reviewed extensively. Here, we turn our attention to the larger, in number and size, long non-coding RNAs (lncRNAs), and review their evolutionary complexity and the growing evidence for their diverse mechanisms of action and functional roles in basic molecular and cellular biology and in human disease. In contrast to the focus on in-silico and expression studies in existing lncRNA literature, we emphasize direct evidence for lncRNA function, presenting experimental approaches and strategies for systematic characterization of lncRNA activities, with applications to known gene regulatory networks and diseases.
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Affiliation(s)
- Leonard Lipovich
- Department of Neurology, Wayne State University, Detroit, MI, USA.
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Kumar RP, Senthilkumar R, Singh V, Mishra RK. Repeat performance: how do genome packaging and regulation depend on simple sequence repeats? Bioessays 2010; 32:165-74. [PMID: 20091758 DOI: 10.1002/bies.200900111] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Non-coding DNA has consistently increased during evolution of higher eukaryotes. Since the number of genes has remained relatively static during the evolution of complex organisms, it is believed that increased degree of sophisticated regulation of genes has contributed to the increased complexity. A higher proportion of non-coding DNA, including repeats, is likely to provide more complex regulatory potential. Here, we propose that repeats play a regulatory role by contributing to the packaging of the genome during cellular differentiation. Repeats, and in particular the simple sequence repeats, are proposed to serve as landmarks that can target regulatory mechanisms to a large number of genomic sites with the help of very few factors and regulate the linked loci in a coordinated manner. Repeats may, therefore, function as common target sites for regulatory mechanisms involved in the packaging and dynamic compartmentalization of the chromatin into active and inactive regions during cellular differentiation.
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Affiliation(s)
- Ram Parikshan Kumar
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Abdolmaleky HM, Zhou JR, Thiagalingam S, Smith CL. Epigenetic and pharmacoepigenomic studies of major psychoses and potentials for therapeutics. Pharmacogenomics 2008; 9:1809-23. [DOI: 10.2217/14622416.9.12.1809] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Individuals with neuropsychiatric diseases have epigenetic programming disturbances, both in the brain, which is the primary affected organ, and in secondary tissues. Epigenetic modulations are molecular modifications made to DNA, RNA and proteins that fine-tune genotype into phenotype and do not include DNA base changes. For instance, gene-expression modulation is linked to epigenetic codes in chromatin that consist of post-replication DNA methylation and histone protein modifications (e.g., methylation, acetylation and so on), particularly in gene-promoter regions. Epigenetic coding is modulated globally, and in a gene-specific manner by environmental exposures that include nutrition, toxins, drugs and so on. Analysis of epigenetic aberrations in diseases helps to identify dysfunctional genes and pathways, establish more robust cause–effect relationships than genetic studies alone, and identify new pharmaceutical targets and drugs, including nucleic acid reagents such as inhibitory RNAs. The emerging science of pharmacoepigenomics can impact the treatment of psychiatric and other complex diseases. In fact, some therapeutics now in use target epigenetic programming. In the near future, epigenetic interventions should help stabilize affected individuals and lead to prevention strategies.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Laboratory of Nutrition and Metabolism at BIDMC, Harvard Medical School, Boston, MA, USA
- Biomedical Engineering Department, Boston University, USA
- Department of Medicine, Genetics & Genomics, Boston University School of Medicine, USA
- Department of Psychiatry and Tehran Psychiatric Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Jin-Rong Zhou
- Laboratory of Nutrition and Metabolism at BIDMC, Harvard Medical School, Boston, MA, USA
| | - Sam Thiagalingam
- Department of Medicine, Genetics & Genomics, Boston University School of Medicine, USA
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