Development of GEBRET: a web-based analysis tool for retroelements in primate genomes |
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Authors: | Hong-Seok Ha Woo-Keun Chung Kung Ahn Jin-Han Bae Sang-Je Park Jae-Woo Moon Kyu-Hwi Nam Kyudong Han Hwan-Gue Cho Heui-Soo Kim |
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Institution: | 1. Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 609-735, Korea 2. Department of Computer Science and Engineering, Pusan National University, Busan, 609-735, Korea 3. Department of Nanobiomedical Science & WCU Research Center, Dankook University, Cheonan, 330-714, Korea
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Abstract: | Retroelements play important roles in primate evolution. Specifically, human endogenous retroviruses (HERVs) and Alu elements are primate-specific retroelements. In addition, SVA elements belong to the youngest family of hominid non-long terminal repeat (LTR) retrotransposons. Retroelements can affect adjacent gene expression, supplying cis-regulatory elements, splice sites, and poly-A signals. We developed a database, GEnome-wide Browser for RETroelement (GEBRET, http://neobio.cs.pusan.ac.kr/~gebre/), for comparing the distribution of primate-specific retroelements and adjacent genes. GEBRET database components include 47,381 HERVs, 53,924 Alus and 4639 SVAs in five primate genomes of human, chimpanzee, orangutan, rhesus macaque, and marmoset. Host genes located upstream of a retroelement were also visualized and classified as five categories (0.0, 0.5, 1.0, 2.0, and 3.0Kb). Our results suggest that retroelements preferentially integrate into the distal promoter region relative to the core promoter region. GEBRET database is designed to investigate the distribution of retroelements (HERVs, Alus and SVAs) in the primate genomes that have been sequenced. Our software will be useful in the field to study the impact of retroelements on primate genome evolution. |
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