Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome
Abstract Background In population ecology, the concept of reproductive potential denotes the most vital indicator of chances to produce and sustain a healthy descendant until his/her reproductive maturity under the best conditions. This concept links quality of life and longevity of an individual wi...
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BMC
2020-10-01
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Series: | BMC Genetics |
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Online Access: | http://link.springer.com/article/10.1186/s12863-020-00896-6 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mikhail Ponomarenko Maxim Kleshchev Petr Ponomarenko Irina Chadaeva Ekaterina Sharypova Dmitry Rasskazov Semyon Kolmykov Irina Drachkova Gennady Vasiliev Natalia Gutorova Elena Ignatieva Ludmila Savinkova Anton Bogomolov Ludmila Osadchuk Alexandr Osadchuk Dmitry Oshchepkov |
spellingShingle |
Mikhail Ponomarenko Maxim Kleshchev Petr Ponomarenko Irina Chadaeva Ekaterina Sharypova Dmitry Rasskazov Semyon Kolmykov Irina Drachkova Gennady Vasiliev Natalia Gutorova Elena Ignatieva Ludmila Savinkova Anton Bogomolov Ludmila Osadchuk Alexandr Osadchuk Dmitry Oshchepkov Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome BMC Genetics Reproductive potential Human Y chromosome Gene Promoter TATA box |
author_facet |
Mikhail Ponomarenko Maxim Kleshchev Petr Ponomarenko Irina Chadaeva Ekaterina Sharypova Dmitry Rasskazov Semyon Kolmykov Irina Drachkova Gennady Vasiliev Natalia Gutorova Elena Ignatieva Ludmila Savinkova Anton Bogomolov Ludmila Osadchuk Alexandr Osadchuk Dmitry Oshchepkov |
author_sort |
Mikhail Ponomarenko |
title |
Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome |
title_short |
Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome |
title_full |
Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome |
title_fullStr |
Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome |
title_full_unstemmed |
Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome |
title_sort |
disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human y chromosome as a self-domestication syndrome |
publisher |
BMC |
series |
BMC Genetics |
issn |
1471-2156 |
publishDate |
2020-10-01 |
description |
Abstract Background In population ecology, the concept of reproductive potential denotes the most vital indicator of chances to produce and sustain a healthy descendant until his/her reproductive maturity under the best conditions. This concept links quality of life and longevity of an individual with disease susceptibilities encoded by his/her genome. Female reproductive potential has been investigated deeply, widely, and comprehensively in the past, but the male one has not received an equal amount of attention. Therefore, here we focused on the human Y chromosome and found candidate single-nucleotide polymorphism (SNP) markers of male reproductive potential. Results Examining in silico (i.e., using our earlier created Web-service SNP_TATA_Z-tester) all 1206 unannotated SNPs within 70 bp proximal promoters of all 63 Y-linked genes, we found 261 possible male-reproductive-potential SNP markers that can significantly alter the binding affinity of TATA-binding protein (TBP) for these promoters. Among them, there are candidate SNP markers of spermatogenesis disorders (e.g., rs1402972626), pediatric cancer (e.g., rs1483581212) as well as male anxiety damaging family relationships and mother’s and children’s health (e.g., rs187456378). First of all, we selectively verified in vitro both absolute and relative values of the analyzed TBP–promoter affinity, whose Pearson’s coefficients of correlation between predicted and measured values were r = 0.84 (significance p < 0.025) and r = 0.98 (p < 0.025), respectively. Next, we found that there are twofold fewer candidate SNP markers decreasing TBP–promoter affinity relative to those increasing it, whereas in the genome-wide norm, SNP-induced damage to TBP–promoter complexes is fourfold more frequent than SNP-induced improvement (p < 0.05, binomial distribution). This means natural selection against underexpression of these genes. Meanwhile, the numbers of candidate SNP markers of an increase and decrease in male reproductive potential were indistinguishably equal to each other (p < 0.05) as if male self-domestication could have happened, with its experimentally known disruptive natural selection. Because there is still not enough scientific evidence that this could have happened, we discuss the human diseases associated with candidate SNP markers of male reproductive potential that may correspond to domestication-related disorders in pets. Conclusions Overall, our findings seem to support a self-domestication syndrome with disruptive natural selection by male reproductive potential preventing Y-linked underexpression of a protein. |
topic |
Reproductive potential Human Y chromosome Gene Promoter TATA box |
url |
http://link.springer.com/article/10.1186/s12863-020-00896-6 |
work_keys_str_mv |
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doaj-1233d8bed5054110bad9b8ca1ba4d17d2020-11-25T03:09:36ZengBMCBMC Genetics1471-21562020-10-0121S111710.1186/s12863-020-00896-6Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndromeMikhail Ponomarenko0Maxim Kleshchev1Petr Ponomarenko2Irina Chadaeva3Ekaterina Sharypova4Dmitry Rasskazov5Semyon Kolmykov6Irina Drachkova7Gennady Vasiliev8Natalia Gutorova9Elena Ignatieva10Ludmila Savinkova11Anton Bogomolov12Ludmila Osadchuk13Alexandr Osadchuk14Dmitry Oshchepkov15Institute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of SciencesAbstract Background In population ecology, the concept of reproductive potential denotes the most vital indicator of chances to produce and sustain a healthy descendant until his/her reproductive maturity under the best conditions. This concept links quality of life and longevity of an individual with disease susceptibilities encoded by his/her genome. Female reproductive potential has been investigated deeply, widely, and comprehensively in the past, but the male one has not received an equal amount of attention. Therefore, here we focused on the human Y chromosome and found candidate single-nucleotide polymorphism (SNP) markers of male reproductive potential. Results Examining in silico (i.e., using our earlier created Web-service SNP_TATA_Z-tester) all 1206 unannotated SNPs within 70 bp proximal promoters of all 63 Y-linked genes, we found 261 possible male-reproductive-potential SNP markers that can significantly alter the binding affinity of TATA-binding protein (TBP) for these promoters. Among them, there are candidate SNP markers of spermatogenesis disorders (e.g., rs1402972626), pediatric cancer (e.g., rs1483581212) as well as male anxiety damaging family relationships and mother’s and children’s health (e.g., rs187456378). First of all, we selectively verified in vitro both absolute and relative values of the analyzed TBP–promoter affinity, whose Pearson’s coefficients of correlation between predicted and measured values were r = 0.84 (significance p < 0.025) and r = 0.98 (p < 0.025), respectively. Next, we found that there are twofold fewer candidate SNP markers decreasing TBP–promoter affinity relative to those increasing it, whereas in the genome-wide norm, SNP-induced damage to TBP–promoter complexes is fourfold more frequent than SNP-induced improvement (p < 0.05, binomial distribution). This means natural selection against underexpression of these genes. Meanwhile, the numbers of candidate SNP markers of an increase and decrease in male reproductive potential were indistinguishably equal to each other (p < 0.05) as if male self-domestication could have happened, with its experimentally known disruptive natural selection. Because there is still not enough scientific evidence that this could have happened, we discuss the human diseases associated with candidate SNP markers of male reproductive potential that may correspond to domestication-related disorders in pets. Conclusions Overall, our findings seem to support a self-domestication syndrome with disruptive natural selection by male reproductive potential preventing Y-linked underexpression of a protein.http://link.springer.com/article/10.1186/s12863-020-00896-6Reproductive potentialHumanY chromosomeGenePromoterTATA box |