Gene Diversification and Transcript Variants by Transposable Elements

1. Human Genome Build 35.1 ` Poly A signal and site analysis RefSeq mRNA cDNA dbEST Gene Gene clustering used by UniGene clustering information RepeatMasker Repeat fused?Yes SIM4 Putative poly A signal search Signal existed?Yes Putative signal with repeat fused Poly A tail search Signal existed? NoYes Only signal data Signal and putative tail data Database Premature polyadenylation signal Promoter 3’UTR AAAAn TSD ORF1 ORF2 TSD 5’UTR Antisense promoter Premature polyadenylation site LINE LTR SINE DNA SD U3 R U5 R MA CA NC PR RT RnaseH IN SU TM U3 U5 R 2841 1068 4335 1138 5’ UTR gag pro pol env 3’ UTR Primer binding site Hormone response element PolyA signal Search for name and accession number U3 R U5 Enhancer Promoter Gene Diversification and Transcript Variants by Transposable Elements Un-Jong Jo1, Dae-Soo Kim1, Tae-Hyung Kim1, Jae-Won Huh2 and Heui-Soo Kim1,2 1PBBRC, Interdisciplinary Research Program of Bioinformatics, Pusan National University, Busan 2Divition of Biological Science, College of Natural Sciences, Pusan National University, Busan http://www.primate.or.kr ABSTRACT During the primate evolution, many different retroelement had integrated into the primate genome and followed by the diversification of gene. Among various transposable elements, LTR and LINE have been reported to have polyadenylation signal for their transcription. SINE also has a potential ability providing the polyadenylation signal if it inserted in 3’ UTR region of gene. The integration of transposable elements which control capacity of the transcription termination results in different transcripts. We found various fused transcripts with transposable element at transcript terminal region, indicating that transposable elements are associated with transcription termination for the alternative splicing. Fusion types were divided by the four types (Type I, Type II, Type II, Type III, and Type IV). Known 12 canonical polyadenylation siganls were used for the analysis of final exon fused by transposable elements. Most of candidate fusion genes were revealed to have more than two polyadenylation signals. We construct a database used by these data set. Database provides expressed information and also our data suggests that transposable elements seem to be main resources to make different splicing pattern in the transcript termination region by providing the polyadenylation signals. It can be accessed at http://www.primate.or.kr/polyadb/. INTRODUCTION Table 2. Composition of exon fused repeat containing putative poly A signal (A) (A) (B) Search forchromosomenumber Search fortransposable elements Fig. 1. Structure of (A) LINE and (B) LTR element MATERIALS AND METHODS (B) Gene information Distribution of Transposable element Expression Transcript alignment information Information fortransposable element EST information andontology Fig. 2. Flow chart of the 3’ UTR expression analysis Fig. 3. Web interface for search menu (A) and result. (B) RESULTS AND DISCUSSION REFERENCES Table 1. Statistics on 3’ repeat fused region 1. Daiqing Liao. Thomas Pavelitz, Alan M. Weiner. 1998. Characterization of noverl class of interspersed LTR elements in primate genomes: Structure, genomic distribution, and evolution. J. Mol. Evol. 46: 649-6602. Dan E. Krane and Ross C. Hardison. 1990. Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals. Mol. Biol. Evol. 7(1):1-8. Repeat fused Signal in repeat fusion region Putative poly A tail in repeat fusion region 8357 5430 4171