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Vasiliev G, Chadaeva I, Rasskazov D, Ponomarenko P, Sharypova E, Drachkova I, Bogomolov A, Savinkova L, Ponomarenko M, Kolchanov N, Osadchuk A, Oshchepkov D, Osadchuk L. A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes. Int J Mol Sci 2021; 22:2346. [PMID: 33652917 PMCID: PMC7956675 DOI: 10.3390/ijms22052346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq data to compare the effect of co-directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common ancestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene-markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson's χ2 test p < 0.001, Fisher's exact test p < 0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial distribution), thus enforcing the norm (wild type).
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Affiliation(s)
- Gennady Vasiliev
- Novosibirsk State University, 630090 Novosibirsk, Russia;
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Irina Drachkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Alexander Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ludmila Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
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Abstract
Sophisticated analyses of current human populations compared to a high-coverage Neandertal genome sequence indicate that, contrary to the previous consensus, African genomes carry a small but significant amount of Neandertal-specific DNA. This indicates back-migration into Africa of modern humans (carrying some Neandertal sequences) and underlines the complexity of ancient human migrations.
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Jordan B. [Human skin pigmentation: more surprises]. Med Sci (Paris) 2019; 35:385-387. [PMID: 31038119 DOI: 10.1051/medsci/2019064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Careful GWAS analysis of a group of mixed-ancestry Latino-American individuals reveals the role of a new "light" variant of the MSFD12 gene which appears to originate in some of the Asian populations that migrated into the Americas 15,000 years ago. This indicates convergent evolution of sparsely pigmented skin at high latitudes, and highlights the interest of performing GWAS studies in non-European populations.
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Affiliation(s)
- Bertrand Jordan
- UMR 7268 ADÉS, Aix-Marseille, Université/EFS/CNRS; - CoReBio PACA, case 901, Parc scientifique de Luminy, 13288 Marseille Cedex 09, France
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