Identification of chimpanzee-specific endogenous retrovirus
through comparative genomics
Seyoung Mun and Kyudong Han*
Department of Nanobiomedical Science & WCU Research Center, Dankook University.,
Anseo-dong, Cheonan 330-714, Republic of Korea
Endogenous retoroviruses (ERVs) are eukaryotic transposable elements and exist as a
provirus in vertebrates including primates. It is known that human endogenous retroviruses
(HERVs) are classified into various subfamilies, consisting of nearly ~4.3% of the human
genome. Among the HERV subfamilies, HERV-K is the youngest subfamily. The HERV-K
element consists of an internal region of three genes (gag, pol, and env) and long terminal
repeats (LTRs) locating on either side of the internal region. The LTRs of full-length HERV-K
elements contain many regulatory sequences, such as promoter, enhancer and transcription
factor binding sites. Many studies the HERV-K elements have been conducted in the human
genome but not in other primates. Here, we first tried to identify chimpanzee-specific
endogenous retrovirus (PtERV) which stands for pan troglodyte endogenous retrovirus.
Through the comparative genomics, we detected 255 PtERV elements from the chimpanzee
reference genome sequence; 132, 112, and 11 out of the elements were full-length,PtERVs,
solo LTRs, and truncated PtERV elements, respectively. To further analyze the full-length
PtERV elements, we conducted PCR amplification and sequenced the PCR products. In
addition, we examined their phylogenetic relationships using various computational methods.
Our results showed that the chimpanzee-specific PtERV element is one of the sources
modifying the chimpanzee genome and thus causing chimpanzee genomic variations.