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Remnants of SIRE1 retrotransposons in human genome?

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Abstract

Evolution is unaimed changes in time that a genome is shaped by a collection of random mutations, recombination, integrations, and reorganizations. Transposable elements (TEs) are mobile fragments representing a major portion of most eukaryotic genomes, and are therefore considered as a key player in evolution. They are one of the main sources of genetic variability and have a large impact on genome structure and stability in eukaryotes. In this study, the plant SIRE1 retrotransposon insertions were demonstrated in the human genome by using barley SIRE1 interretrotransposon amplified polymorphism PCR (IRAP-PCR) primers. According to the IRAP-PCR analysis, different distribution patterns were observed for 24 participants used in this study. The polymorphism ratios of SIRE1 were calculated, and among all samples they were detected between 0 to 38%. Similarly, internal domains and LTR sequences of SIRE1 were investigated by sequencing. Partial GAG, RT and ENV gene sequences were detected in the human genome by performing sequence and bioinformatic analyses. According to the bioinformatic analysis, partial SIRE1 ENV sequences were interestingly detected in both human and chimpanzee chromosome 1. Partial SIRE1 ENV sequences in chromosome 1 were also found to be associated with neuroblastoma breakpoint family members’ (NBPFs) in humans. Polymorphic TE insertions in the human genome may be an essential source of natural genetic variation with subtle effects on genome regulation, providing considerable source material for ongoing human evolution.

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Acknowledgement

Scientific Research Projects Coordination Unit of Istanbul University (grant number FDK-2017-22142) has supported this work.

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  1. Buket Cakmak Guner and Elif Karlik contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Institute of Science, Istanbul University, 34134, Vezneciler, Istanbul, Turkey

    Buket Cakmak Guner, Elif Karlik & Nermin Gozukirmizi

  2. Department of Molecular Biology and Genetics, Faculty of Art and Science, Avrasya University, 61000, Trabzon, Turkey

    Buket Cakmak Guner

  3. Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istinye University, 34010, Istanbul, Turkey

    Elif Karlik

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Guner, B.C., Karlik, E. & Gozukirmizi, N. Remnants of SIRE1 retrotransposons in human genome?. J Genet 102, 10 (2023). https://doi.org/10.1007/s12041-022-01398-3

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