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Chirkov S, Sheveleva A, Tsygankova S, Slobodova N, Sharko F, Petrova K, Mitrofanova I. First Report and Complete Genome Characterization of Cherry Virus A and Little Cherry Virus 1 from Russia. Plants (Basel) 2023; 12:3295. [PMID: 37765462 PMCID: PMC10534684 DOI: 10.3390/plants12183295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Virus diseases affect the yield and fruit quality and shorten the productive life of stone fruits (Prunus spp. in the family Rosaceae). Of over fifty known viruses infecting these crops, cherry virus A (CVA) is among the most common, and little cherry virus 1 (LChV1) is one of the most economically important. Using high-throughput sequencing, full-length genomes of CVA and LChV1 isolates, found on interspecies hybrids in the Prunus collection of the Nikita Botanical Gardens, Russia, were sequenced, assembled, and characterized. CVA was found in the P. cerasifera × P. armeniaca hybrid and in phylogenetic analysis clustered with non-cherry virus isolates. The LChV1 isolate Stepnoe was detected in ((P. cerasifera Ehrh. × P. armeniaca L.) × P. brigantiaca Vill.) trihybrid suggesting that both P. cerasifera and P. brigantiaca potentially can be the LChV1 hosts. The isolate Stepnoe was most closely related to the Greece isolate G15_3 from sweet cherry, sharing 77.3% identity at the nucleotide level. Possibly, the highly divergent Russian isolate represents one more phylogroup of this virus. This is the first report of CVA and LChV1 from Russia, expanding the information on their geographical distribution and genetic diversity.
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Affiliation(s)
- Sergei Chirkov
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Anna Sheveleva
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Svetlana Tsygankova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
| | - Natalia Slobodova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
- Faculty of Biology and Biotechnology, HSE University, 101000 Moscow, Russia
| | - Fedor Sharko
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
- Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina Petrova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (S.T.); (N.S.); (F.S.); (K.P.)
- Research Center for Medical Genetics, 115552 Moscow, Russia
| | - Irina Mitrofanova
- Tsitsin Main Botanical Garden of Russian Academy of Sciences, 127276 Moscow, Russia;
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2
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Slobodova N, Sharko F, Gladysheva-Azgari M, Petrova K, Tsiupka S, Tsiupka V, Boulygina E, Rastorguev S, Tsygankova S. Genetic Diversity of Common Olive ( Olea europaea L.) Cultivars from Nikita Botanical Gardens Collection Revealed Using RAD-Seq Method. Genes (Basel) 2023; 14:1323. [PMID: 37510228 PMCID: PMC10379327 DOI: 10.3390/genes14071323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
In different countries, interest in the commercial cultivation of the olive has recently greatly increased, which has led to the expansion of its range. The Crimean Peninsula is the northern limit of the common olive (Olea europaea L.) range. A unique collection of common olive's cultivars and hybrids has been collected in the Nikitsky Botanical Gardens (NBG). The aim of this study was to assess the genetic diversity of 151 samples (total of several biological replicates of 46 olive cultivars including 29 introduced and 11 indigenous genotypes) using the ddRAD sequencing method. Structural analysis showed that the studied samples are divided into ten groups, each of which mainly includes cultivars of the same origin. Cultivars introduced to the Crimean Peninsula from different regions formed separate groups, while local cultivars joined different groups depending on their origin. Cultivars of Crimean origin contain admixtures of mainly Italian and Caucasian cultivars' genotypes. Our study showed that the significant number of Crimean cultivars contains an admixture of the Italian cultivar "Coreggiolo". Genetic analysis confirmed the synonymy for the cv. "Otur" and "Nikitskaya 2", but not for the other four putative synonyms. Our results revealed the genetic diversity of the olive collection of NBG and provided references for future research studies, especially in selection studies for breeding programs.
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Affiliation(s)
- Natalia Slobodova
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
- Faculty of Biology and Biotechnology, HSE University, Moscow 101000, Russia
| | - Fedor Sharko
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | | | | | - Sergey Tsiupka
- Nikita Botanical Gardens-National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Russia
| | - Valentina Tsiupka
- Nikita Botanical Gardens-National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Russia
| | - Eugenia Boulygina
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Sergey Rastorguev
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
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3
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Sharko F, Slobodova N, Boulygina E, Cheprasov M, Gladysheva-Azgari M, Tsygankova S, Rastorguev S, Novgorodov G, Boeskorov G, Grigorieva L, Hwang WS, Tikhonov A, Nedoluzhko A. Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia. Genes (Basel) 2023; 14:genes14030700. [PMID: 36980972 PMCID: PMC10047931 DOI: 10.3390/genes14030700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023] Open
Abstract
Paleoclimatic changes during the Pleistocene–Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller’s sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene–Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the “young” specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.
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Affiliation(s)
- Fedor Sharko
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Faculty of Biology and Biotechnology, HSE University, 101000 Moscow, Russia
| | - Eugenia Boulygina
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Maksim Cheprasov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
- Federal Research Centre “The Yakut Scientific Centre of the Siberian Branch of the Russian Academy of Sciences”, 677980 Yakutsk, Russia
| | - Maria Gladysheva-Azgari
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Svetlana Tsygankova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- Laboratory of Experimental Embryology, Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Gavril Novgorodov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of the Russian Academy of Sciences, 677007 Yakutsk, Russia
| | - Lena Grigorieva
- Center of Molecular Paleontology, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Woo Suk Hwang
- UAE Biotech Research Center, Abu Dhabi 30310, United Arab Emirates
- Department of Biology, North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Alexei Tikhonov
- Lazarev Mammoth Museum, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | - Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint Petersburg, Russia
- Correspondence:
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Boulygina E, Sharko F, Cheprasov M, Gladysheva-Azgari M, Slobodova N, Tsygankova S, Rastorguev S, Grigorieva L, Kopp M, Fernandes JMO, Novgorodov G, Boeskorov G, Protopopov A, Hwang WS, Tikhonov A, Nedoluzhko A. Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear ( Ursus arctos) Population during the Holocene. Genes (Basel) 2022; 13:1961. [PMID: 36360198 PMCID: PMC9689912 DOI: 10.3390/genes13111961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 09/14/2023] Open
Abstract
Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.
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Affiliation(s)
- Eugenia Boulygina
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Sharko
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Maksim Cheprasov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Maria Gladysheva-Azgari
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Svetlana Tsygankova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Lena Grigorieva
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Martina Kopp
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Jorge M. O. Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Gavril Novgorodov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of Russian 5 Academy of Sciences, 677007 Yakutsk, Russia
| | - Albert Protopopov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Academy of Sciences of Sakha (Yakutia), 677007 Yakutsk, Russia
| | - Woo-Suk Hwang
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- UAE Biotech Research Center, Abu Dhabi 30310, United Arab Emirates
| | - Alexei Tikhonov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Zoological Institute Russian Academy of Sciences, 190121 Saint-Petersburg, Russia
| | - Artem Nedoluzhko
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint-Petersburg, Russia
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Chirkov S, Sheveleva A, Tsygankova S, Sharko F, Mitrofanova I. Characterization of Divergent Grapevine Badnavirus 1 Isolates Found on Different Fig Species (Ficus spp.). Plants 2022; 11:plants11192532. [PMID: 36235398 PMCID: PMC9573714 DOI: 10.3390/plants11192532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]
Abstract
Fig mosaic disease is spread worldwide and is believed to have a viral etiology. Divergent isolates of grapevine badnavirus 1 (GBV1), named fGBV1, were discovered on Ficus carica, F. palmata, F. virgata, and F. afghanistanica in the fig germplasm collection of the Nikita Botanical Gardens, Russia, expanding the list of viruses infecting this crop. The complete genomes of five fGBV1 isolates from F. carica and F. palmata trees were determined using high-throughput and Sanger sequencing. The genomes comprised 7283 base pairs, contained four overlapping open reading frames, were 99.7 to 99.9% identical to each other, and related to GBV1 (83.2% identity). The reverse transcriptase RNase H genome regions of fGBV1 and GBV1 share 84.6% identity, indicating that fGBV1 is a divergent isolate of GBV1, which was found on the new natural hosts from a different family (Moraceae). Further, fGBV1-specific primers were developed to detect the virus using RT-PCR. Survey of 47 trees, belonging to four fig species and 14 local and introduced F. carica cultivars, showed the high fGBV1 prevalence in the collection (93.6%), including trees with no obvious symptoms of fig mosaic disease.
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Affiliation(s)
- Sergei Chirkov
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence:
| | - Anna Sheveleva
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | | | - Fedor Sharko
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Irina Mitrofanova
- Tsitsin Main Botanical Garden of Russian Academy of Sciences, 127276 Moscow, Russia
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Nedoluzhko A, Sharko F, Tsygankova S, Boulygina E, Slobodova N, Teslyuk A, Galindo-Villegas J, Rastorguev S. Intergeneric hybridization of two stickleback species leads to introgression of membrane-associated genes and invasive TE expansion. Front Genet 2022; 13:863547. [PMID: 36092944 PMCID: PMC9452749 DOI: 10.3389/fgene.2022.863547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Interspecific hybridization has occurred relatively frequently during the evolution of vertebrates. This process usually abolishes reproductive isolation between the parental species. Moreover, it results in the exchange of genetic material and can lead to hybridogenic speciation. Hybridization between species has predominately been observed at the interspecific level, whereas intergeneric hybridization is rarer. Here, using whole-genome sequencing analysis, we describe clear and reliable signals of intergeneric introgression between the three-spined stickleback (Gasterosteus aculeatus) and its distant mostly freshwater relative the nine-spined stickleback (Pungitius pungitius) that inhabit northwestern Russia. Through comparative analysis, we demonstrate that such introgression phenomena apparently take place in the moderate-salinity White Sea basin, although it is not detected in Japanese sea stickleback populations. Bioinformatical analysis of the sites influenced by introgression showed that they are located near transposable elements, whereas those in protein-coding sequences are mostly found in membrane-associated and alternative splicing-related genes.
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Affiliation(s)
- Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, Saint Petersburg, Russia
- Limited Liability Company ELGENE, Moscow, Russia
| | - Fedor Sharko
- Limited Liability Company ELGENE, Moscow, Russia
- Laboratory of Vertebrate Genomics and Epigenomics, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Laboratory of Bioinformatics and Big Data Analysis, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Svetlana Tsygankova
- Laboratory of Eukaryotic Genomics, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Eugenia Boulygina
- Laboratory of Eukaryotic Genomics, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Natalia Slobodova
- Laboratory of Eukaryotic Genomics, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Anton Teslyuk
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Jorge Galindo-Villegas
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- *Correspondence: Jorge Galindo-Villegas, ; Sergey Rastorguev,
| | - Sergey Rastorguev
- Limited Liability Company ELGENE, Moscow, Russia
- Laboratory of Bioinformatics and Big Data Analysis, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
- *Correspondence: Jorge Galindo-Villegas, ; Sergey Rastorguev,
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Gladysheva-Azgari M, Petrova K, Tsygankova S, Mitrofanova I, Smykov A, Boulygina E, Slobodova N, Rastorguev S, Sharko F. A de novo genome assembly of cultivated Prunus persica cv. ‘Sovetskiy’. PLoS One 2022; 17:e0269284. [PMID: 35714114 PMCID: PMC9205522 DOI: 10.1371/journal.pone.0269284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/18/2022] [Indexed: 11/19/2022] Open
Abstract
Prunus persica is one of the main stone fruit crops in Crimea and southern Russia. The P. persica genome has recently been sequenced and annotated in good quality. However, for a deeper assessment of the peach genome, it is necessary to include in the research other cultivars that are in the collection of the Nikitsky Botanical Garden. The cultivars of the Nikitsky Botanical Garden are unique and differ from Western European and American ones, as they are derived from cultivars and forms originating from Central Asian, North Caucasian, Transcaucasian and Eastern European countries. In this paper, we present the assembly of the P. persica cv. ’Sovetskiy’ genome obtained using Oxford Nanopore long reads and Illumina short reads by hybrid assembly methods. The assembled genome of P. persica cv. ’Sovetskiy’ is 206.26 MB in 226 scaffolds, with N50 24 Mb, including 8 chromosomes. It contains 27140 coding genes, 26973 (99.38%) of which are annotated in at least one functional database. More than 36.05% of the genome regions were identified as repeating elements.
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Affiliation(s)
| | | | | | - Irina Mitrofanova
- Nikita Botanical Gardens – National Scientific Centre of the Russian Academy of Sciences, Yalta, Russia
| | - Anatoliy Smykov
- Nikita Botanical Gardens – National Scientific Centre of the Russian Academy of Sciences, Yalta, Russia
| | | | | | | | - Fedor Sharko
- National Research Center "Kurchatov Institute", Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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Tsygankova S, Komova D, Boulygina E, Slobodova N, Sharko F, Rastorguev S, Gladysheva-Azgari M, Koroleva D, Smol’yaninova A, Tatarnikova S, Obuchova T, Nedoluzhko A, Gabeeva N, Zvonkov E. Non-GCB Diffuse Large B-Cell Lymphoma With an Atypical Disease Course: A Case Report and Clinical Exome Analysis. World J Oncol 2022; 13:38-47. [PMID: 35317330 PMCID: PMC8913013 DOI: 10.14740/wjon1436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/31/2021] [Indexed: 11/27/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid tumor among other non-Hodgkin lymphomas (30-40% of all cases). This type of lymphoma is characterized by significant differences in treatment response and the heterogeneity of clinical traits. Approximately 60% of patients are cured using standard chemotherapy (CT), while in 10-15% of cases, the tumor is characterized by an extremely aggressive course and resistance to even the most high-dose programs with autologous stem cell transplantation (auto-SCT). The activated B-cell (ABC) subtype of DLBCL is characterized by poor prognosis. Here, we describe a clinical case of diffuse ABC-DLBCL with an atypical disease course. Complete remission was achieved after four courses of CT, followed by autologous hematopoietic stem cell transplantation (auto-HSCT). However, early relapse occurred 2 months after the completion of treatment. According to the results of cytogenetic studies, significant chromosome breakdowns were observed. Exome sequencing allowed for the detection of several novel mutations that affect components of the NOTCH2 and NF-κB signaling pathways, a number of epigenetic regulators (KMT2D, CREBBP, EP300, ARID1A, MEF2B), as well as members of the immunoglobulin superfamily (CD58 and CD70). Whether these mutations were the result of therapy or were originally present in the lymphoid tumor remains unclear. Nevertheless, the introduction of genomic technologies into clinical practice is important for making a diagnosis and developing a DLBCL treatment regimen with the use of targeted drugs.
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Affiliation(s)
- Svetlana Tsygankova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
- These authors contributed equally
- Corresponding Author: Svetlana Tsygankova, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia.
| | - Daria Komova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
- These authors contributed equally
| | - Eugenia Boulygina
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Sharko
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Daria Koroleva
- National Medical Hematology Research Center, 125167 Moscow, Russia
| | | | | | - Tatiana Obuchova
- National Medical Hematology Research Center, 125167 Moscow, Russia
| | - Artem Nedoluzhko
- Moscow Healthcare Department, Mental-Health Clinic No. 1 Named After N.A. Alexeev, 115191 Moscow, Russia
| | - Nelli Gabeeva
- National Medical Hematology Research Center, 125167 Moscow, Russia
| | - Eugene Zvonkov
- National Medical Hematology Research Center, 125167 Moscow, Russia
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Sharko F, Gladysheva-Azgari M, Tsygankova S, Mitrofanova I, Boulygina E, Slobodova N, Smykov A, Rastorguev S, Nedoluzhko A. The complete chloroplast genome sequence of cultivated Prunus persica cv. 'Sovetskiy'. Mitochondrial DNA B Resour 2021; 6:2882-2883. [PMID: 34532577 PMCID: PMC8439202 DOI: 10.1080/23802359.2021.1972861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The peach (Prunus persica L. Batsch) is one of the important stone fruit crops in the Crimea Peninsula and the southern part of Russia. The complete chloroplast genome of the peach cultivar ‘Sovetskiy’ is published in this paper. The chloroplast genome size is 157,756 bp. It contains 126 genes, including 81 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The chloroplast genome also contains a large single-copy region of 85,960 bp, a small single-copy (SSC) region of 19,045 bp, and two inverted repeats regions of 26,375 bp and 26,372 bp. The overall base composition of the genome in descending order is 31.2% – A, 32.1% – T, 18.7% – C, and 18.0% – G. The total GC content of the chloroplast genome is 36.7%. Maximum-likelihood phylogenetic analysis involving nine chloroplast genomes of the Prunus genus revealed a separate cluster for P. persica and its possible landrace – P. ferganensis.
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Affiliation(s)
- Fedor Sharko
- National Research Center "Kurchatov Institute", Moscow, Russia
| | | | | | - Irina Mitrofanova
- Nikita Botanical Gardens - National Scientific Centre of the Russian Academy of Sciences, Yalta, Russia
| | | | | | - Anatoliy Smykov
- Nikita Botanical Gardens - National Scientific Centre of the Russian Academy of Sciences, Yalta, Russia
| | | | - Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Obukhova P, Tsygankova S, Chinarev A, Shilova N, Nokel A, Kosma P, Bovin N. Are there specific antibodies against Neu5Gc epitopes in the blood of healthy individuals? Glycobiology 2021; 30:395-406. [PMID: 31897477 DOI: 10.1093/glycob/cwz107] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
Strong discrepancies in published data on the levels and epitope specificities of antibodies against the xenogenic N-glycolyl forms of sialoglycans (Hanganutziu-Deicher Neu5Gcɑ2-3Galβ1-4Glc and related antigens) in healthy donors prompted us to carry out a systematic study in this area using the printed glycan array and other methods. This article summarizes and discusses our published and previously unpublished data, as well as publicly available data from the Consortium for Functional Glycomics. As a result, we conclude that (1) the level of antibodies referred to as anti-Neu5Gc in healthy individuals is low; (2) there are antibodies that seem to interact with Neu5Gc-containing epitopes, but in fact they recognize internal fragments of Neu5Gc-containing glycans (without sialic acids), which served as antigens in the assays used and; (3) a population capable of interacting specifically with Neu5Gc (it does not bind the corresponding NAc analogs) does exist, but it binds the monosaccharide Neu5Gc better than the entire glycans containing it. In other words, in healthy donors, there are populations of antibodies capable of binding the Neu5Gc monosaccharide or the inner core -Galβ1-4Glc, but very few true anti-Neu5Gcɑ2-3Galβ1-4Glc antibodies, i.e., antibodies capable of specifically recognizing the entire trisaccharide.
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Affiliation(s)
- Polina Obukhova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia.,Federal State Budget Institution, National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 4 Oparin str., 117997, Moscow, Russia
| | - Svetlana Tsygankova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia
| | - Alexander Chinarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia
| | - Nadezhda Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia.,Federal State Budget Institution, National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 4 Oparin str., 117997, Moscow, Russia.,Semiotik LLC, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia
| | - Alexey Nokel
- Federal State Budget Institution, National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, 4 Oparin str., 117997, Moscow, Russia.,Semiotik LLC, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences, 18 Muthgasse, 1190 Vienna, Austria, and
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia.,Auckland University of Technology, 55 Wellesley Street East, 1010, Auckland, New Zealand
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11
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Nedoluzhko A, Sharko F, Tsygankova S, Boulygina E, Ibragimova A, Teslyuk A, Galindo-Villegas J, Rastorguev S. Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin. Heliyon 2021; 7:e06160. [PMID: 33604473 PMCID: PMC7875830 DOI: 10.1016/j.heliyon.2021.e06160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/16/2020] [Accepted: 01/27/2021] [Indexed: 11/26/2022] Open
Abstract
Interspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples of G. aculeatus and P. pungitius and subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.
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Affiliation(s)
- Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Corresponding author.
| | - Fedor Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Eugenia Boulygina
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Amina Ibragimova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anton Teslyuk
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Jorge Galindo-Villegas
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Corresponding author.
| | - Sergey Rastorguev
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
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12
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Dobrochaeva K, Khasbiullina N, Shilova N, Knirel Y, Obukhova P, Nokel A, Kunetskiy R, Tsygankova S, Bello-Gil D, Costa C, Mañez R, Bovin N. Specificity profile of αGal antibodies in αGalT KO mice as probed with comprehensive printed glycan array: Comparison with human anti-Galili antibodies. Xenotransplantation 2021; 28:e12672. [PMID: 33432698 DOI: 10.1111/xen.12672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The α1,3-galactosyltransferase gene-knockout (GalT KO) mice are able to produce natural anti-αGal antibodies apparently without any specific immunization. GalT KO mice are commonly used as a model immunological system for studying anti-αGal responses to Gal-positive xenografts in human. In this study, we compared the specificity of mouse and human αGal antibodies to realize the adequacy of the murine model. METHODS Using hapten-specific affinity chromatography antibodies against Galα1-3Galβ1-4GlcNAcβ epitope were isolated from both human and GalT KO mice blood sera. Specificity of isolated antibodies was determined using a printed glycan array (PGA) containing 400 mammalian glycans and 200 bacterial polysaccharides. RESULTS The quantity of isolated specific anti-Galα antibodies corresponds to a content of <0.2% of total Ig, which is an order of magnitude lower than that generally assumed for both human and murine peripheral blood immunoglobulin, with a high predominance of IgM over IgG (95% vs 5%). Analysis using a printed glycan array has demonstrated that (a) antibodies from both species bind not only the Galα1-3Galβ1-4GlcNAcβ epitope, but also unrelated glycans; (b) particularly, for human (but not mouse) antibodies the best binders appear to be bacterial polysaccharides; (c) the profile of mouse antibodies is broader, it is noteworthy that they recognize a variety of human blood group B epitopes and even glycans without the α-galactosyl residue. CONCLUSIONS We believe that the mouse model should be used cautiously in xenotransplantation experiments when the fine epitope specificity of antibodies is critical.
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Affiliation(s)
- Kira Dobrochaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nailya Khasbiullina
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.,National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russia
| | - Nadezhda Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russia.,Semiotik LLC, Moscow, Russia
| | - Yuriy Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Polina Obukhova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russia
| | - Alexey Nokel
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russia.,Semiotik LLC, Moscow, Russia
| | - Roman Kunetskiy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Svetlana Tsygankova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Bello-Gil
- Infectious Pathology and Transplantation Division, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
| | - Cristina Costa
- Infectious Pathology and Transplantation Division, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
| | - Rafael Mañez
- Infectious Pathology and Transplantation Division, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,School of Engineering, Computer & Mathematical Sciences, Auckland University of Technology, Auckland, New Zealand
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13
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Chirkov S, Tsygankova S, Rastorguev S, Mitrofanova I, Chelombit S, Bulygina E, Slobodova N, Sharko F. First report of fig mosaic virus on fig in Russia. Plant Dis 2021; 105. [PMID: 33417494 DOI: 10.1094/pdis-11-20-2463-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fig mosaic virus (FMV) (genus Emaravirus in the family Fimoviridae) is considered the etiological agent of fig mosaic disease (FMD) that is recorded in most of the fig growing areas with an average global infection rate of 33%. The multipartite FMV genome is comprised of six negative monocistronic ssRNAs, each of which is separately encapsidated (Preising et al. 2020). Although FMD-like symptoms, which include mosaic, chlorotic ringspots, and oak leaf patterns, were observed in approximately a third of 400 fig accessions in the Nikita Botanical Gardens, Yalta, Russia (Mitrofanova et al. 2016), FMV has not been identified as the causal agent of the disease. In June of 2020, total RNA was isolated from symptomatic leaves of 59 thirty two-year-old trees representing 31 local and 27 introduced Ficus carica L. cultivars and a single F. pseudocarica Miq. tree using RNeasy Plant Mini kit (Qiagen, USA). FMV was tested by RT-PCR using primer sets E5 (Elbeaino et al. 2009) and EMARAVGP (Walia et al. 2009), which amplify a 302-bp fragment of RNA1 and a 468-bp fragment of RNA2, respectively. PCR products of the expected sizes were generated in all samples, indicating a high FMV incidence in the plantings. The genome sequences of FMV isolates from F. carica cvs. Bleuet, Kraps di Hersh, Smena, Temri, and F. pseudocarica (Fig. S1) were determined by high-throughput sequencing on MiSec Illumina platform. Double-stranded RNA was isolated from FMV-positive leaves using Viral Gene-spin™ Viral DNA/RNA Extraction Kit (iNtRON, Korea), followed by cDNA library preparation with the NEBNext® Ultra™ II RNA Library Prep Kit (New England Biolabs, USA). In average, 695,000 quality-filtered 150 bp pair-ended reads per a library were produced and used in a de novo assembly using metaSpades program version 3.14 (Nurk et al. 2017). In each of five samples, BLASTn analysis found six FMV-related contigs. The contigs spanned 99 to 100% of corresponding genomic segments of the most closely related isolates. In addition to FMV, fig cryptic virus-related contigs were also detected in some samples. The FMV contigs covering RNA1 to RNA6 had the highest identity to corresponding genomic segments of isolates AM941711 (96.5 to 96.6%), FM864225 (94.4 to 94.6%), FM991954 (97.9 to 98.2%), AB697863 (96.4 to 96.6%), AB697879 (93.3 to 93.4%), and AB697895 (95.4 to 97.0%), respectively. Five Russian isolates shared 99.2 to 100% nucleotide sequence identity, depending on the genomic segment. Their sequences were deposited in GenBank under accession numbers MW201216 to MW201230 and MW208662 to MW208676. Phylogenetic analysis of six ORFs showed that ORF1 to ORF3 and ORF6 of the Russian isolates clustered with FMV isolates from Italy while ORF4 grouped with the isolate JTT-Pa (AB697863) from Japan (Fig. S2). ORF5 of the Russian isolates formed a separate cluster with the isolates SB1 and SB2 from Serbia and JTT-Vi from Japan (AB697879 to AB697884). Incongruency of phylogenetic relationship among the genomic segments suggests reassortment among ancestors of the Russian FMV isolates. In addition, similar to the SB1, SB2 and JTT-Vi, ORF5 of the Russian isolates encodes a protein of 486 amino acid (aa) residues in contrast to the corresponding protein of Italian isolates consisting of 502 aa. To the best of our knowledge, this is the first report of FMV in Russia. This finding not only expands the information on the geographical distribution of FMV, but also extends knowledge on F. pseudocarica as a natural host of the virus.
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Affiliation(s)
- Sergei Chirkov
- Nikita Botanical Gardens - National Scientific Center, Yalta, Russian Federation
- Lomonosov Moscow State University, Virology Department, Moscow, Russian Federation;
| | - Svetlana Tsygankova
- National Research Center Kurchatov Institute, 68636, Moskva, Moskva, Russian Federation;
| | - Sergey Rastorguev
- National Research Center Kurchatov Institute, 68636, Moskva, Moskva, Russian Federation;
| | - Irina Mitrofanova
- Nikita Botanical Gardens - National Scientific Center, Yalta, Russian Federation;
| | - Svetlana Chelombit
- Nikita Botanical Gardens - National Scientific Center, Yalta, Russian Federation;
| | - Eugenia Bulygina
- National Research Center Kurchatov Institute, 68636, Moskva, Moskva, Russian Federation;
| | - Natalia Slobodova
- National Research Center Kurchatov Institute, 68636, Moskva, Moskva, Russian Federation;
| | - Fedor Sharko
- National Research Center Kurchatov Institute, 68636, Moskva, Moskva, Russian Federation;
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14
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Obukhova P, Tsygankova S, Chinarev A, Shilova N, Nokel A, Kosma P, Bovin N. Corrigendum to: Are there specific antibodies against Neu5Gc epitopes in the blood of healthy individuals? Glycobiology 2020; 30:415. [DOI: 10.1093/glycob/cwaa004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 11/14/2022] Open
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15
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Ershov NI, Mordvinov VA, Prokhortchouk EB, Pakharukova MY, Gunbin KV, Ustyantsev K, Genaev MA, Blinov AG, Mazur A, Boulygina E, Tsygankova S, Khrameeva E, Chekanov N, Fan G, Xiao A, Zhang H, Xu X, Yang H, Solovyev V, Lee SMY, Liu X, Afonnikov DA, Skryabin KG. New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes. BMC Genomics 2019; 20:399. [PMID: 31117933 PMCID: PMC6530080 DOI: 10.1186/s12864-019-5752-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
Background The three epidemiologically important Opisthorchiidae liver flukes Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, are believed to harbour similar potencies to provoke hepatobiliary diseases in their definitive hosts, although their populations have substantially different ecogeographical aspects including habitat, preferred hosts, population structure. Lack of O. felineus genomic data is an obstacle to the development of comparative molecular biological approaches necessary to obtain new knowledge about the biology of Opisthorchiidae trematodes, to identify essential pathways linked to parasite-host interaction, to predict genes that contribute to liver fluke pathogenesis and for the effective prevention and control of the disease. Results Here we present the first draft genome assembly of O. felineus and its gene repertoire accompanied by a comparative analysis with that of O. viverrini and Clonorchis sinensis. We observed both noticeably high heterozygosity of the sequenced individual and substantial genetic diversity in a pooled sample. This indicates that potency of O. felineus population for rapid adaptive response to control and preventive measures of opisthorchiasis is higher than in O. viverrini and C. sinensis. We also have found that all three species are characterized by more intensive involvement of trans-splicing in RNA processing compared to other trematodes. Conclusion All revealed peculiarities of structural organization of genomes are of extreme importance for a proper description of genes and their products in these parasitic species. This should be taken into account both in academic and applied research of epidemiologically important liver flukes. Further comparative genomics studies of liver flukes and non-carcinogenic flatworms allow for generation of well-grounded hypotheses on the mechanisms underlying development of cholangiocarcinoma associated with opisthorchiasis and clonorchiasis as well as species-specific mechanisms of these diseases. Electronic supplementary material The online version of this article (10.1186/s12864-019-5752-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nikita I Ershov
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia.
| | | | - Egor B Prokhortchouk
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia. .,ZAO Genoanalytica, 1 Leninskie Gory street, Moscow, 119234, Russia.
| | - Mariya Y Pakharukova
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Konstantin V Gunbin
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Kirill Ustyantsev
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Mikhail A Genaev
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Alexander G Blinov
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Alexander Mazur
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia
| | | | | | | | - Nikolay Chekanov
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia
| | - Guangyi Fan
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - An Xiao
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - He Zhang
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Huanming Yang
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Victor Solovyev
- Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xin Liu
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Konstantin G Skryabin
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia.,Federal Research Center Kurchatov Institute, Moscow, Russia
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16
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Arabadzhieva D, Gyurova A, Alexandrova L, Chinarev A, Tsygankova S, Tuzikov A, Khristov K, Ranguelov B, Mileva E. Smart Complex Fluids Based on Two-Antennary Oligoglycines. ChemSusChem 2019; 12:672-683. [PMID: 30548560 DOI: 10.1002/cssc.201802308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Antennary oligoglycines are synthetic products, obtained as a result of preliminary molecular design. Equal-length antennae are built of glycine residues joined through the C end to an oligoamine branching core with an amine group at the N terminus exposed outside. The results of systematic research on the properties of aqueous solutions containing two-antennary oligoglycine with four glycine portions are reported. The central feature is the competition between amphiphilic self-assembly and formation of polyglycine II motifs. A combined procedure is developed to characterize bulk and interfacial structures and coatings. It includes registration of bulk aggregates, examination of interfacial layers at solution/air and solution/solid boundaries, drainage, and stability of liquid films. The obtained results provide new insight into the structure-property relationships in these smart fluids and give essential hints about key factors allied to possible applications in medicine, pharmaceuticals, and environmental protection.
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Affiliation(s)
- Dimi Arabadzhieva
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl.11, 1113, Sofia, Bulgaria
| | - Anna Gyurova
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl.11, 1113, Sofia, Bulgaria
| | - Lidia Alexandrova
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl.11, 1113, Sofia, Bulgaria
| | - Alexander Chinarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul/ Muklukho-Maklaya 16/10, 2117497, Moscow, Russia
| | - Svetlana Tsygankova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul/ Muklukho-Maklaya 16/10, 2117497, Moscow, Russia
| | - Alexander Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul/ Muklukho-Maklaya 16/10, 2117497, Moscow, Russia
| | - Khristo Khristov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl.11, 1113, Sofia, Bulgaria
| | - Bogdan Ranguelov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl.11, 1113, Sofia, Bulgaria
| | - Elena Mileva
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl.11, 1113, Sofia, Bulgaria
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17
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Triska P, Chekanov N, Stepanov V, Khusnutdinova EK, Kumar GPA, Akhmetova V, Babalyan K, Boulygina E, Kharkov V, Gubina M, Khidiyatova I, Khitrinskaya I, Khrameeva EE, Khusainova R, Konovalova N, Litvinov S, Marusin A, Mazur AM, Puzyrev V, Ivanoshchuk D, Spiridonova M, Teslyuk A, Tsygankova S, Triska M, Trofimova N, Vajda E, Balanovsky O, Baranova A, Skryabin K, Tatarinova TV, Prokhortchouk E. Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe. BMC Genet 2017; 18:110. [PMID: 29297395 PMCID: PMC5751809 DOI: 10.1186/s12863-017-0578-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. RESULTS We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the "Finno-Ugric" origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main "core", being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the "Great Siberian Vortex" directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts. CONCLUSIONS Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations.
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MESH Headings
- Algorithms
- Asia
- DNA
- Datasets as Topic
- Emigration and Immigration/history
- Ethnicity/genetics
- Europe
- Female
- Genetic Variation
- Genetics, Population
- Genotyping Techniques
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Male
- Russia
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Affiliation(s)
- Petr Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nikolay Chekanov
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- "Genoanalytica" CJSC, Moscow, Russia
| | - Vadim Stepanov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Konstantin Babalyan
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | | | - Vladimir Kharkov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | - Irina Khitrinskaya
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Ekaterina E Khrameeva
- "Genoanalytica" CJSC, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, Russia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Sergey Litvinov
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Andrey Marusin
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Alexandr M Mazur
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
| | - Valery Puzyrev
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Dinara Ivanoshchuk
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maria Spiridonova
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Anton Teslyuk
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Svetlana Tsygankova
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Martin Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Natalya Trofimova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Edward Vajda
- Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, USA
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
| | - Ancha Baranova
- Research Centre for Medical Genetics, Moscow, Russia
- School of Systems Biology, George Mason University, Fairfax, VA, USA
- Atlas Biomed Group, Moscow, Russia
| | - Konstantin Skryabin
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- Russian Scientific Centre "Kurchatov Institute", Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Tatarinova
- Vavilov Institute of General Genetics, Moscow, Russia.
- School of Systems Biology, George Mason University, Fairfax, VA, USA.
- Atlas Biomed Group, Moscow, Russia.
- Department of Biology, University of La Verne, La Verne, CA, USA.
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Egor Prokhortchouk
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
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18
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Nedoluzhko A, Sharko F, Boulygina E, Tsygankova S, Sokolov A, Mazur A, Polilov A, Prokhortchouk E, Skryabin K. The complete mitochondrial genome of the smallest known free-living insect Scydosella musawasensis. Mitochondrial DNA B Resour 2016; 1:171-172. [PMID: 33644334 PMCID: PMC7871854 DOI: 10.1080/23802359.2016.1149785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mitochondrial genome of the smallest known free-living insect Scydosella musawasensis (Polilov, 2015) is published in this paper. The mitochondrial DNA (mtDNA) is 14 719 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes and 21 tRNA genes. The overall base composition of the genome in descending order was 40.59% – A, 13.85% – C, 36.82% – T and 8.73% – G, with a significant AT bias of 77.41%.
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Affiliation(s)
- Artem Nedoluzhko
- Genome Analysis Laboratory, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Fedor Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Eugenia Boulygina
- Genome Analysis Laboratory, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Svetlana Tsygankova
- Genome Analysis Laboratory, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Alexey Sokolov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey Polilov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Egor Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Skryabin
- Genome Analysis Laboratory, National Research Centre "Kurchatov Institute", Moscow, Russia.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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19
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Zhenilo S, Khrameeva E, Tsygankova S, Zhigalova N, Mazur A, Prokhortchouk E. Individual genome sequencing identified a novel enhancer element in exon 7 of the CSFR1 gene by shift of expressed allele ratios. Gene 2015; 566:223-8. [PMID: 25913741 DOI: 10.1016/j.gene.2015.04.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 04/16/2015] [Accepted: 04/20/2015] [Indexed: 10/23/2022]
Abstract
The sequencing of individual genetic information may provide a powerful tool for elucidating the mechanism by which individual SNPs affect promoter function. Here, we assessed the genome of a Russian male that was previously sequenced. The RNA-Seq data from blood cells revealed 234 candidate transcripts with shifts of greater than 1.5-fold from equal biallelic transcription. Of these genes, the CSF1R gene had variations in genic regions that affected the association of RORalpha with its target binding site in vivo. The results of a reporter assay confirmed that a single nucleotide substitution, rs2228422, within the RORalpha recognition motif altered the ability of the enhancer to regulate CSF1R gene transcription. Notably, 31% of Europeans and only 3% of Asians are homozygous for a RORalpha responsive "A" allele, but no association with diseases of rs2228422 has been found thus far.
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Affiliation(s)
- S Zhenilo
- Center "Bioengineering" Russian Academy of Sciences, 117312, Prospect 60-let Oktyabrya, 7-1, Moscow, Russia
| | - E Khrameeva
- Center "Bioengineering" Russian Academy of Sciences, 117312, Prospect 60-let Oktyabrya, 7-1, Moscow, Russia
| | - S Tsygankova
- Center "Bioengineering" Russian Academy of Sciences, 117312, Prospect 60-let Oktyabrya, 7-1, Moscow, Russia
| | - N Zhigalova
- Center "Bioengineering" Russian Academy of Sciences, 117312, Prospect 60-let Oktyabrya, 7-1, Moscow, Russia
| | - A Mazur
- Center "Bioengineering" Russian Academy of Sciences, 117312, Prospect 60-let Oktyabrya, 7-1, Moscow, Russia
| | - E Prokhortchouk
- Center "Bioengineering" Russian Academy of Sciences, 117312, Prospect 60-let Oktyabrya, 7-1, Moscow, Russia.
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