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Karamysheva T, Romanenko S, Makunin A, Rajičić M, Bogdanov A, Trifonov V, Blagojević J, Vujošević M, Orishchenko K, Rubtsov N. New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis. Cells 2021; 10:cells10071819. [PMID: 34359988 PMCID: PMC8305704 DOI: 10.3390/cells10071819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.
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Affiliation(s)
- Tatyana Karamysheva
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1332)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.R.); (V.T.)
| | | | - Marija Rajičić
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Alexey Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.R.); (V.T.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Jelena Blagojević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Mladen Vujošević
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, 11060 Belgrade, Serbia; (M.R.); (J.B.); (M.V.)
| | - Konstantin Orishchenko
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikolay Rubtsov
- Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (K.O.); (N.R.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
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Okulova NM, Bogdanov AS, Baskevich MI, Orlov VN, Popova YV, Antonets NV, Lavrenchenko LA. Skull Sizes and Proportions in Western Palearctic Wood Mice (Sylvaemus, Muridae, Rodentia) from Eastern Europe: 2. Intraspecific Variability. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019080119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Okulova NM, Bogdanov AS, Baskevich MI, Orlov VN, Antonets NV, Popova YV, Lavrenchenko LA. Skull Sizes and Proportions in Western Palearctic Wood Mice (Sylvaemus, Muridae, Rodentia) from Eastern Europe: 1. Interspecific Variability. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019080107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rubtsova NV, Karamysheva TV, Rubtsov NB. Clusters of Repetitive DNA Sequences in Chromosomes of Voles of the Subgenus Microtus (Microtus, Arvicolidae). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419090126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sequence Composition and Evolution of Mammalian B Chromosomes. Genes (Basel) 2018; 9:genes9100490. [PMID: 30309007 PMCID: PMC6211034 DOI: 10.3390/genes9100490] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
B chromosomes (Bs) revealed more than a hundred years ago remain to be some of the most mysterious elements of the eukaryotic genome. Their origin and evolution, DNA composition, transcriptional activity, impact on adaptiveness, behavior in meiosis, and transfer to the next generation require intensive investigations using modern methods. Over the past years, new experimental techniques have been applied and helped us gain a deeper insight into the nature of Bs. Here, we consider mammalian Bs, taking into account data on their DNA sequencing, transcriptional activity, positions in nuclei of somatic and meiotic cells, and impact on genome functioning. Comparative cytogenetics of Bs suggests the existence of different mechanisms of their formation and evolution. Due to the long and complicated evolvement of Bs, the similarity of their morphology could be explained by the similar mechanisms involved in their development while the difference between Bs even of the same origin could appear due to their positioning at different stages of their evolution. A complex analysis of their DNA composition and other features is required to clarify the origin and evolutionary history of Bs in the species studied. The intraspecific diversity of Bs makes this analysis a very important element of B chromosome studies.
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Grigoryeva OO, Stakheev VV, Orlov VN. Mitochondrial Evidence of Refugial Distribution of the Pygmy Field Mouse Sylvaemus uralensis Pall. (Rodentia, Muridae) in the Northwestern Caucasus. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418030055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Jetybayev IY, Bugrov AG, Buleu OG, Bogomolov AG, Rubtsov NB. Origin and Evolution of the Neo-Sex Chromosomes in Pamphagidae Grasshoppers through Chromosome Fusion and Following Heteromorphization. Genes (Basel) 2017; 8:genes8110323. [PMID: 29137168 PMCID: PMC5704236 DOI: 10.3390/genes8110323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/16/2022] Open
Abstract
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family. The homologous regions of the neo-sex chromosomes were determined in closely related species with the painting procedure and image analysis with application of the Visualization of the Specific Signal in Silico software package. Results of these analyses and distribution of C-positive regions in the neo-sex chromosomes revealed details of the heteromorphization of the neo-sex chromosomes in species from both phylogenetic lineages of Pamphagidae grasshoppers. The hypothetical mechanism of the neo-Y degradation was suggested. It includes expansion of different repeats from the proximal neo-Y chromosome region by inversions, spreading them towards distal region. Amplification of these repeats leads to formation of C-positive regions and elimination of the C-negative regions located between them.
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Affiliation(s)
- Ilyas Yerkinovich Jetybayev
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
| | - Alexander Gennadievich Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Olesya Georgievna Buleu
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Anton Gennadievich Bogomolov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Nikolay Borisovich Rubtsov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
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Karamysheva TV, Torgasheva AA, Yefremov YR, Bogomolov AG, Liehr T, Borodin PM, Rubtsov NB. Spatial organization of fibroblast and spermatocyte nuclei with different B-chromosome content in Korean field mouse, Apodemus peninsulae (Rodentia, Muridae). Genome 2017; 60:815-824. [PMID: 28732174 DOI: 10.1139/gen-2017-0029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Korean field mouse (Apodemus peninsulae) shows a wide variation in the number of B chromosomes composed of constitutive heterochromatin. For this reason, it provides a good model to study the influence of the number of centromeres and amount of heterochromatin on spatial organization of interphase nuclei. We analyzed the three-dimensional organization of fibroblast and spermatocyte nuclei of the field mice carrying a different number of B chromosomes using laser scanning microscopy and 3D fluorescence in situ hybridization. We detected a co-localization of the B chromosomes with constitutive heterochromatin of the chromosomes of the basic set. We showed a non-random distribution of B chromosomes in the spermatocyte nuclei. Unpaired B chromosomes showed a tendency to occur in the compartment formed by the unpaired part of the XY bivalent.
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Affiliation(s)
- Tatyana V Karamysheva
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Anna A Torgasheva
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Yaroslav R Yefremov
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton G Bogomolov
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Thomas Liehr
- c Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Pavel M Borodin
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikolay B Rubtsov
- a Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,b Novosibirsk State University, 630090 Novosibirsk, Russia
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Rajičić M, Romanenko SA, Karamysheva TV, Blagojević J, Adnađević T, Budinski I, Bogdanov AS, Trifonov VA, Rubtsov NB, Vujošević M. The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)-Break rules but keep playing the game. PLoS One 2017; 12:e0172704. [PMID: 28329013 PMCID: PMC5362141 DOI: 10.1371/journal.pone.0172704] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022] Open
Abstract
B chromosomes (Bs) are known for more than hundred years but their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed by whole DNA amplification, DNA probe generation, and fluorescent in situ hybridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA probes followed by FISH on metaphase chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific probes for the first time. We revealed homology of DNA derived from the analyzed B chromosomes to the pericentromeric region (PR) of sex chromosomes and subtelomeric region of two pairs of small autosomes, but lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their number per individual or the great geographic distance between examined populations from the Balkan Peninsula (Serbia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B chromosomes in A. flavicollis have a unique common origin from the PR of sex chromosomes, and/or similar evolutionary pattern.
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Affiliation(s)
- M Rajičić
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - S A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk Russia
| | - T V Karamysheva
- Institute of Cytology and Genetics, SB RAS, Novosibirsk Russia
| | - J Blagojević
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - T Adnađević
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - I Budinski
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - A S Bogdanov
- Koltzov Institute of Developmental Biology, RAS, Moscow Russia
| | - V A Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk Russia
| | - N B Rubtsov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk Russia
| | - M Vujošević
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
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Rubtsov NB, Karamysheva TV, Bogdanov AS, Kartavtseva IV, Bochkarev MN, Iwasa MA. Comparative analysis of DNA homology in pericentric regions of chromosomes of wood mice from genera Apodemus and Sylvaemus. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415120091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Vakurin AA, Kartavtseva IV, Korablev VP, Pavlenko MV. Some features of cytogenetic differentiation of striped hamsters, Cricetulus barabensis and Cricetulus pseudogriseus (Rodentia, Cricetidae). BIOL BULL+ 2014. [DOI: 10.1134/s1062359014090088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rudra M, Bahadur M. Heterochromatin variation among the populations of Mus terricolor Blyth, 1851 (Rodentia, Muridae) chromosome type I. COMPARATIVE CYTOGENETICS 2013; 7:139-151. [PMID: 24260696 PMCID: PMC3833757 DOI: 10.3897/compcytogen.v7i2.4136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
Twenty five to thirty specimens each from ten populations of Mus terricolor of the Terai and the Dooars regions of the Darjeeling foothills of West Bengal were cytogenetically analyzed using C-banding. Results showed intra- and inter- population variation of C-band positive heterochromatin ranging from very large blocks to minute amounts or even complete absence of heterochromatin. Large blocks of centromeric C-bands were found in Bidhan Nagar, Garidhura, Malbazar, Nagrakata and Maynaguri populations in most of the autosomes, while the rest of the populations had large blocks of C-bands on a few autosomes only. Such intra- and inter- population variation may be due to accumulation of C-positive heterochromatin, which has not got fixed homogeneously in all autosome pairs. X-chromosomes invariably possess a C-banded short arm a telomeric C-band at the distal end of the long arm in all populations. The entire Y-chromosome was C-band positive with slight population differences in staining intensity. The results suggest quantitative as well as qualitative variation of C-positive heterochromatin.
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Affiliation(s)
- Mahua Rudra
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of North Bengal, Siliguri-734013, West Bengal, India
| | - Min Bahadur
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of North Bengal, Siliguri-734013, West Bengal, India
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Bogdanov AS, Stakheev VV, Zykov AE, Yakimenko VV, Mal’kova MG. Genetic variation and differentiation of wood mice from the genus Sylvaemus inferred from sequencing of the cytochrome oxidase subunit 1 gene fragment. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412020044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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