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Pascual-Torner M, Carrero D, Pérez-Silva JG, Álvarez-Puente D, Roiz-Valle D, Bretones G, Rodríguez D, Maeso D, Mateo-González E, Español Y, Mariño G, Acuña JL, Quesada V, López-Otín C. Comparative genomics of mortal and immortal cnidarians unveils novel keys behind rejuvenation. Proc Natl Acad Sci U S A 2022; 119:e2118763119. [PMID: 36037356 PMCID: PMC9459311 DOI: 10.1073/pnas.2118763119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 07/06/2022] [Indexed: 12/13/2022] Open
Abstract
Turritopsis dohrnii is the only metazoan able to rejuvenate repeatedly after its medusae reproduce, hinting at biological immortality and challenging our understanding of aging. We present and compare whole-genome assemblies of T. dohrnii and the nonimmortal Turritopsis rubra using automatic and manual annotations, together with the transcriptome of life cycle reversal (LCR) process of T. dohrnii. We have identified variants and expansions of genes associated with replication, DNA repair, telomere maintenance, redox environment, stem cell population, and intercellular communication. Moreover, we have found silencing of polycomb repressive complex 2 targets and activation of pluripotency targets during LCR, which points to these transcription factors as pluripotency inducers in T. dohrnii. Accordingly, we propose these factors as key elements in the ability of T. dohrnii to undergo rejuvenation.
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Affiliation(s)
- Maria Pascual-Torner
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
- Observatorio Marino de Asturias, Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Dido Carrero
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - José G. Pérez-Silva
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Diana Álvarez-Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - David Roiz-Valle
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Gabriel Bretones
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - David Rodríguez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Daniel Maeso
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Elena Mateo-González
- Observatorio Marino de Asturias, Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Yaiza Español
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Guillermo Mariño
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, 33006, Spain
- Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011, Spain
| | - José Luis Acuña
- Observatorio Marino de Asturias, Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, 33006, Spain
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Regeneration and reprogramming. Curr Opin Genet Dev 2012; 22:485-93. [PMID: 23084810 DOI: 10.1016/j.gde.2012.09.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/24/2012] [Accepted: 09/17/2012] [Indexed: 01/14/2023]
Abstract
Recent reprogramming studies indicate that mammalian, somatic cells have the potential to achieve pluripotent states and undergo cell type switching. Such cellular traits are observed under natural conditions in animals that regenerate complex organs. A number of invertebrates display the amazing trait of whole body regeneration. Underlying this trait is the maintenance of pluripotent cells in somatic tissue, and molecular studies indicate the use of common players associated with pluripotency and germ cell properties between these invertebrates and mammalian pluripotent cells. In regenerative vertebrates, heart regeneration, lens regeneration, and retinal regeneration provide good examples of dedifferentiation and transdifferentiation. The molecular factors associated with these phenomena are discussed.
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Senthilkumar R, Mishra RK. Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit. BMC Genomics 2009; 10:549. [PMID: 19930571 PMCID: PMC2784810 DOI: 10.1186/1471-2164-10-549] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 11/20/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polycomb group (PcG) proteins maintain expression pattern of genes set early during development. Although originally isolated as regulators of homeotic genes, PcG members play a key role in epigenetic mechanism that maintains the expression state of a large number of genes. Polycomb (PC) is conserved during evolution and while invertebrates have one PC gene, vertebrates have five or more homologues. It remains unclear if different vertebrate PC homologues have distinct or overlapping functions. We have identified and compared the sequence of PC homologues in various organisms to analyze similarities and differences that shaped the evolutionary history of this key regulatory protein. RESULTS All PC homologues have an N-terminal chromodomain and a C-terminal Polycomb Repressor box. We searched the protein and genome sequence database of various organisms for these signatures and identified approximately 100 PC homologues. Comparative analysis of these sequences led to the identification of a novel insect specific motif and several novel and signature motifs in the vertebrate homologue: two in CBX2 (Cx2.1 and Cx2.2), four in CBX4 (Cx4.1, Cx4.2, Cx4.3 and Cx4.4), three in CBX6 (Cx6.1, Cx6.2 and Cx6.3) and one in CBX8 (Cx8.1). Additionally, adjacent to the chromodomain, all the vertebrate homologues have a DNA binding motif - AT-Hook in case of CBX2, which was known earlier, and 'AT-Hook Like' motif, from this study, in other PC homologues. CONCLUSION Our analysis shows that PC is an ancient gene dating back to pre bilaterian origin that has not only been conserved but has also expanded during the evolution of complexity. Unique motifs acquired by each homologue have been maintained for more than 500 millions years indicating their functional relevance in boosting the epigenetic 'tool kit'. We report the presence of a DNA interaction motif adjacent to chromodomain in all vertebrate PC homologues and suggest a three-way 'PC-histoneH3-DNA' interaction that can restrict nucleosome dynamics. The signature motifs of PC homologues and insect specific motif identified in this study pave the way to understand the molecular basis of epigenetic mechanisms.
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Abstract
In development, cells pass on established gene expression patterns to daughter cells over multiple rounds of cell division. The cellular memory of the gene expression state is termed maintenance, and the proteins required for this process are termed maintenance proteins. The best characterized are proteins of the Polycomb and trithorax Groups that are required for silencing and maintenance of activation of target loci, respectively. These proteins act through DNA elements termed maintenance elements. Here, we re-examine the genetics and molecular biology of maintenance proteins. We discuss molecular models for the maintenance of activation and silencing, and the establishment of epigenetic marks, and suggest that maintenance proteins may play a role in propagating the mark through DNA synthesis.
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Affiliation(s)
- Hugh W Brock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
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Zhang H, Azevedo RBR, Lints R, Doyle C, Teng Y, Haber D, Emmons SW. Global regulation of Hox gene expression in C. elegans by a SAM domain protein. Dev Cell 2003; 4:903-15. [PMID: 12791274 DOI: 10.1016/s1534-5807(03)00136-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polycomb group (PcG)-mediated repression of C. elegans Hox genes has not been demonstrated, and genes homologous to components of one of the PcG complexes (PRC1) have not been identified in the C. elegans genome. We find that a mechanism of general Hox gene repression exists in C. elegans, carried out in part by SOP-2, a protein related to, but not orthologous with, any PcG protein. sop-2 mutations lead to widespread ectopic expression of Hox genes and homeotic transformations. SOP-2 contains a SAM domain, a self-associating protein domain found in other repressors, including a core component of PRC1 and ETS transcription factors. Phylogenetic analysis indicates that this domain is more closely related to those of the ETS family than to those of PcG proteins. The results suggest that global repression of Hox genes has been taken over by a different branch of the SAM domain family during the evolution of nematodes.
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Affiliation(s)
- Hong Zhang
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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