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A comprehensive analysis of chimpanzee (Pan Troglodytes)-specific AluYb8 element

Genes & Genomics 2020년 42권 10호 p.1207 ~ 1213
김송미, 김동희, Imai Hiroo, 이용문, 한규동,
소속 상세정보
김송미 ( Kim Song-Mi ) - Dankook University Department of Nanobiomedical Science
김동희 ( Kim Dong-Hee ) - Dankook University Hospital Department of Anesthesiology and Pain Medicine
 ( Imai Hiroo ) - Kyoto University Primate Research Institute Department of Cellular and Molecular Biology
이용문 ( Lee Yong-Moon ) - Dankook University College of Medicine Department of Pathology
한규동 ( Han Kyu-Dong ) - Dankook University Department of Nanobiomedical Science

Abstract


Background: Alu elements are most abundant retrotransposons with?>?1.2 million copies in the primate genome. AluYb8 subfamily was diverged from AluY lineage, and has accumulated eight diagnostic mutations and 7-bp duplication during primate evolution. A total of 1851 AluYb copies are present in the human genome, and most of them are human-specific. On the other hand, only a few AluYb8 copies were identified in the chimpanzee genome by previous studies on AluYb8. The significantly different number of species-specific AluYb8 elements between human and chimpanzee might result from the incompletion of chimpanzee reference genome sequences at the time of the previous study.

Objective: AluYb8 elements could generate genomic structural variations in the chimpanzee genome. This study aimed to identify and characterize chimpanzee-specific AluYb elements using the most updated chimpanzee reference genome sequences (Jan. 2018, panTro6).

Methods: To identify chimpanzee-specific AluYb8, we carried out genomic comparison with non-chimpanzee primate genome using the UCSC table browser. In addition, chimpanzee-specific AluYb8 candidates were manually inspected and experimentally verified using PCR and Sanger sequencing.

Results: Among a total of 231 chimpanzee-specific AluYb8 candidates, 11 of the candidates are chimpanzee-specific AluYb8, and 29 elements are shared between the chimpanzee and non-chimpanzee primate genomes. Through the sequence analysis of AluYb8 and other Alu subfamilies, we were able to observe various diagnostic mutations and variable length duplications in 7-bp duplication region of AluYb8 element. In addition, we further validated two of the chimpanzee-specific AluYb8 elements (CS8 and CS20) that were not previously discovered by display PCR and Sanger sequencing. Interestingly, we identified a AluYb8 insertion-mediated deletion (CS8 locus) in the chimpanzee genome.

Conclusion: Our study found that AluYb8 elements are much more abundant in the human genome than chimpanzee genome, and that it could be due to the absence of hyperactive “master” AluYb8 elements in the chimpanzee genome.

키워드

Alu elements; AluYb8; Chimpanzee-specific; Retrotransposons

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