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Gene Diversification and Transcript Variantsby 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

MATERIALS AND METHODS

REFERENCES

Fig. 1. Structure of (A) LINE and (B) LTR element

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.

417154308357

Putative poly A tail in repeat fusion region

Signal in repeat fusion regionRepeat fused

Table 1. Statistics on 3’ repeat fused region

1138433510682841

DNASINELTRLINE

Table 2. Composition of exon fused repeat containing putative poly A signal

(A)

(B)

Fig. 2. Flow chart of the 3’ UTR expression analysis

Fig. 3. Web interface for search menu (A) and result. (B)

ORF2ORF1

3’UTR

Antisense promoter

Promoter

Premature polyadenylation site

Premature polyadenylation signal

TSD AAAAn TSD5’UTR

5’ UTRPrimer binding site

SD

gag pro pol env 3’ UTR

U5

RU3RU5 MA CA NC PR RT RnaseHIN SU TM U3RU5

RU3

Hormone response element

EnhancerPromoter

PolyA signal

Search for nameand accession number

Search forchromosomenumber

Search fortransposableelements

(A)

(B)Human Genome Build 35.1

RefSeq

SIM4

Putative poly A signal search

Repeat fused?Yes

Signal existed?Yes

Putative signal with repeat fused

mRNA cDNA dbEST Gene

Gene clustering used by UniGene clustering information

RepeatMasker

Poly A signal and site analysis

Poly A tail search

Signal existed? NoYes

Only signal data

Signal and putative tail data

Database

RESULTS AND DISCUSSION

Gene information

Distribution of Transposable element

Expression

Information fortransposableelement

EST information andontology

Transcript alignmentinformation