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Motta-Neto CC, Marques A, Costa GW, Cioffi MB, Bertollo LA, Soares RX, Scortecci KC, Artoni RF, Molina WF. Differential hypomethylation of the repetitive Tol2/Alu-rich sequences in the genome of Bodianus species (Labriformes, Labridae). COMPARATIVE CYTOGENETICS 2018; 12:145-162. [PMID: 29675141 PMCID: PMC5904366 DOI: 10.3897/compcytogen.v12i2.21830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Representatives of the order Labriformes show karyotypes of extreme conservatism together with others with high chromosomal diversification. However, the cytological characterization of epigenetic modifications remains unknown for the majority of the species. In the family Labridae, the most abundant fishes on tropical reefs, the genomes of the genus Bodianus Bloch, 1790 have been characterized by the occurrence of a peculiar chromosomal region, here denominated BOD. This region is exceptionally decondensed, heterochromatic, argentophilic, GC-neutral and, in contrast to classical secondary constrictions, shows no signals of hybridization with 18S rDNA probes. In order to characterize the BOD region, the methylation pattern, the distribution of Alu and Tol2 retrotransposons and of 18S and 5S rDNA sites, respectively, were analyzed by Fluorescence In Situ Hybridization (FISH) on metaphase chromosomes of two Bodianus species, B. insularis Gomon & Lubbock, 1980 and B. pulchellus (Poey, 1860). Immunolocalization of the 5-methylcytosine revealed hypermethylated chromosomal regions, dispersed along the entire length of the chromosomes of both species, while the BOD regions exhibited a hypomethylated pattern. Hypomethylation of the BOD region is associated with the precise co-location of Tol2 and Alu elements, suggesting their active participation in the regulatory epigenetic process. This evidence underscores a probable differential methylation action during the cell cycle, as well as the role of Tol2/Alu elements in functional processes of fish genomes.
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Affiliation(s)
- Clóvis C. Motta-Neto
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - André Marques
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Gideão W.W.F. Costa
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Marcelo B. Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Paulo, Brazil
| | - Luiz A.C. Bertollo
- Department of Genetics and Evolution, Federal University of São Carlos, São Paulo, Brazil
| | - Rodrigo X. Soares
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Kátia C. Scortecci
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Roberto F. Artoni
- Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Wagner F. Molina
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
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Dyachenko OV, Tarlachkov SV, Marinitch DV, Shevchuk TV, Buryanov YI. Expression of exogenous DNA methyltransferases: application in molecular and cell biology. BIOCHEMISTRY (MOSCOW) 2015; 79:77-87. [PMID: 24794723 DOI: 10.1134/s0006297914020011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
DNA methyltransferases might be used as powerful tools for studies in molecular and cell biology due to their ability to recognize and modify nitrogen bases in specific sequences of the genome. Methylation of the eukaryotic genome using exogenous DNA methyltransferases appears to be a promising approach for studies on chromatin structure. Currently, the development of new methods for targeted methylation of specific genetic loci using DNA methyltransferases fused with DNA-binding proteins is especially interesting. In the present review, expression of exogenous DNA methyltransferase for purposes of in vivo analysis of the functional chromatin structure along with investigation of the functional role of DNA methylation in cell processes are discussed, as well as future prospects for application of DNA methyltransferases in epigenetic therapy and in plant selection.
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Affiliation(s)
- O V Dyachenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Fedoreyeva LI, Smirnova TA, Kolomijtseva GY, Khavinson VK, Vanyushin BF. Interaction of short peptides with FITC-labeled wheat histones and their complexes with deoxyribooligonucleotides. BIOCHEMISTRY (MOSCOW) 2013; 78:166-75. [PMID: 23581987 DOI: 10.1134/s0006297913020053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Judging from fluorescence modulation (quenching), short peptides (Ala-Glu-Asp-Gly, Glu-Asp-Arg, Ala-Glu-Asp-Leu, Lys-Glu-Asp-Gly, Ala-Glu-Asp-Arg, and Lys-Glu-Asp-Trp) bind with FITC-labeled wheat histones H1, H2B, H3, and H4. This results from the interaction of the peptides with the N-terminal histone regions that contain respective and seemingly homologous peptide-binding motifs. Because homologous amino acid sequences in wheat core histones were not found, the peptides seem to bind with some core histone regions having specific conformational structure. Peptide binding with histones and histone-deoxyribooligonucleotide complexes depends on the nature of the histone and the primary structures of the peptides and oligonucleotides; thus, it is site specific. Histones H1 bind preferentially with single-stranded oligonucleotides by homologous sites in the C-terminal region of the protein. Unlike histone H1, the core histones bind predominantly with double-stranded methylated oligonucleotides and methylated DNA. Stern-Volmer constants of interaction of histone H1 and core histones with double-stranded hemimethylated oligonucleotides are higher compared with that of binding with unmethylated ones. DNA or deoxyribooligonucleotides in a complex with histones can enhance or inhibit peptide binding. It is suggested that site-specific interactions of short biologically active peptides with histone tails can serve in chromatin as control epigenetic mechanisms of regulation of gene activity and cellular differentiation.
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Affiliation(s)
- L I Fedoreyeva
- All Russia Research Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, 127550 Moscow, Russia
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Theoretical study of the interaction between 5-methylcytosine and acrylamide. J Mol Model 2012; 18:4447-52. [PMID: 22592385 DOI: 10.1007/s00894-012-1426-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 04/03/2012] [Indexed: 10/28/2022]
Abstract
The hydrogen-bonded complexes between 5-methylcytosine and acrylamide have been investigated using the density function theory (DFT) method. Five stable complexes have been found with no imaginary frequencies. Complex C3 is the most stable one with interaction energies of -69.01 kJ mol(-1) corrected for basis set superposition error (BSSE). The charge change in the process of these complexes formation has also been examined. The atoms in molecules (AIM) theory and natural bond orbital (NBO) method have been performed to investigate the hydrogen bonds involved in all the complexes. The electron density and its corresponding Laplacian at the bond and ring critical points have been analyzed. In C3 complex, there is the largest stabilization energy (18.17 kJ mol(-1)) between N11-H12 antibonding orbital and lone electron pair of O17. It can be seen that the hydrogen bonds play a crucial role in the stability of all the complexes between 5-methylcytosine and acrylamide. The theoretical results could provide helpful information for other researchers in further work.
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Tolmacheva EN, Kashevarova AA, Skryabin NA, Lebedev IN. DNA methylation profile in human placental tissues. Mol Biol 2011. [DOI: 10.1134/s0026893311030198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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