title: Identification of human-specific AluS elements through comparative genomics.
abstract: Mobile elements are responsible for ~45% of the human genome. Among them is the Alu element, accounting for 10% of the human genome (>1.1million copies). Several studies of Alu elements have reported that they are frequently involved in human genetic diseases and genomic rearrangements. In this study, we investigated the AluS subfamily, which is a relatively old Alu subfamily and has the highest copy number in primate genomes. Previously, a set of 263 human-specific AluS insertions was identified in the human genome. To validate these, we compared each of the human-specific AluS loci with its pre-insertion site in other primate genomes, including chimpanzee, gorilla, and orangutan. We obtained 24 putative human-specific AluS candidates via the in silico analysis and manual inspection, and then tried to verify them using PCR amplification and DNA sequencing. Through the PCR product sequencing, we were able to detect two instances of near-parallel Alu insertions in nearby sites that led to computational false negatives. Finally, we computationally and experimentally verified 23 human-specific AluS elements. We reported three alternative Alu insertion events, which are accompanied by filler DNA and/or Alu retrotransposition mediated-deletion. Bisulfite sequencing was carried out to examine DNA methylation levels of human-specific AluS elements. The results showed that fixed AluS elements are hypermethylated compared with polymorphic elements, indicating a possible relation between DNA methylation and Alu fixation in the human genome.
authors.affiliation: Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea.
authors.forename: Jae
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea.
authors.forename: Yun-Ji
authors.initials: YJ
authors.lastname: Kim
authors.affiliation: Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea.
authors.forename: Seyoung
authors.initials: S
authors.lastname: Mun
authors.affiliation: Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea.
authors.forename: Heui-Soo
authors.initials: HS
authors.lastname: Kim
authors.affiliation: Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea. Electronic address: jim97@dankook.ac.kr.
authors.forename: Kyudong
authors.initials: K
authors.lastname: Han
mesh_terms: D000483:Alleles; D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006071:Gorilla gorilla; D006801:Humans; D002679:Pan troglodytes; D011110:Polymorphism, Genetic; D057079:Pongo; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements
keywords: Alu element; Comparative genomics; DNA methylation; Transposable element