Format

Send to

Choose Destination
Genes Genomics. 2019 Mar 18. doi: 10.1007/s13258-019-00794-x. [Epub ahead of print]

A comprehensive analysis of the Baboon-specific full-length LINE-1 retrotransposons.

Lee W1,2, Choi M1,2, Kim S1,2, Tang W3, Kim DH4, Kim HS5, Liang P3, Han K6,7.

Author information

1
Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
2
DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea.
3
Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.
4
Department of Anesthesiology and Pain Management, College of Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
5
Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.
6
Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea. jim97@dankook.ac.kr.
7
DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea. jim97@dankook.ac.kr.

Abstract

BACKGROUND:

Long interspersed elements-1 (LINE-1s or L1s) and Alu elements are most successful retrotransposons that have generated genetic diversity and genomic fluidity in the primate genome. They account for ~ 27.7% of the primate genome. Interestingly, a previous study has shown that the retrotransposition rate of Alu elements is nine times higher in baboons than in humans.

OBJECTIVE:

The expansion of Alu copies could be dependent on the activity of L1-encoded proteins. Thus, we aimed to investigate full-length baboon-specific L1s and characterize structurally and functionally intact baboon-specific L1s (ORF1p/ORF2p and ORF2p only) that could induce trans-mobilization of Alu elements in the baboon genome.

RESULTS:

A total of 673 baboon-specific L1 candidates (> 4 kb) were identified through the comparative genomic analysis. Applying the baboon-specific correction value obtained from the experimental validation, it demonstrated that approximately 446 baboon-specific L1s (> 4 kb) were present in the baboon reference genome (papAnu2). In addition, we observed phylogenetic relationship of the baboon-specific L1s through the neighbor-joining method and they diverged from the L1PA6 consensus sequence. Finally, we identified 36 full-length baboon-specific L1s that were intact both ORF1p and ORF2p.

CONCLUSION:

The number of baboon-specific full-length L1s is fewer than the number of human-specific full-length L1s. Therefore, there is possibility that the "L1 master gene" or "L1 source gene" is more abundant in the baboon genome, or that in trans retrotransposition activity of baboon-specific L1s is relatively stronger than in the other genomes.

KEYWORDS:

Baboon; Baboon-specific; LINE-1; Transposable element

PMID:
30887304
DOI:
10.1007/s13258-019-00794-x

Supplemental Content

Loading ...
Support Center