Evolutionary diversification of DYX1C1 gene transcripts by HERV-H LTR integration event Results & Discussion Abstract DYX1C1 (dyslexia susceptibility 1.
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Evolutionary diversification of DYX1C1 gene Evolutionary diversification of DYX1C1 gene transcripts by HERV-H LTR integration eventtranscripts by HERV-H LTR integration event
Results & Discussion
Abstract
DYX1C1 (dyslexia susceptibility 1 candidate 1) gene on human chromosome 15q21.3 is a candidate gene for developmental dyslexia. The DYX1C1 shows three alternatively spliced transcripts in GenBank database. We found that one of transcripts is related to HERV-H LTR element that could affect the protein-coding region. The HERV-H LTR element on human DYX1C1 gene seems to have been integrated into our common ancestor genome after the divergence of Old World monkeys and New World monkeys. RT-PCR analysis of HERV-H LTR-related transcript shows that five different alternative transcripts are expressed in several human tissues. Five different alternative splicing forms are also identified in various rhesus monkey tissues. From the sequencing analysis of various primate DNA samples, we found the lineage specific tandem repeated sequences of Old World monkeys in protein coding region. However, the formation of tandem repeated sequences did not affect the amino acid sequences. Taken together, integration event of the HERV-H LTR element contributed to the DYX1C1 gene diversification by affecting protein coding region during the primateevolution.………………………………………………………………………..…
Yun-Ji Kim1, Jae-Won Huh1, Dae-Soo Kim2, Hong-Seok Ha1, Kung Ahn1, Ja-Rang Lee1, Min-In Bae1, and Heui-Soo Kim1, 2
1Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea2 PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University,
Busan 609-735, Republic of Korea
http://www.primate.or.kr
Materials & Methods
Plasmid DNA Isolation
Transformation-Inoculation
Ligation
Electrophoresis-Gel purification
Polymerase Chain Reaction (PCR)
Gene Cloning
Genomic DNAs& cDNA
PCR & RT-PCR
Bioinformatics
QIAEX II gel extraction kit(Qiagen)High Pure plasmid isolation kit
Human Monkey
NCBI,BLAST,MEGA3
Introduction
Chr.15
q21.3
NM_001033560.1
10
EXON1
2 3 4 5 6 7 8 9
EXON1 2 3 4 5 6 7 8 9
EXON1 2 3 4 5 6 7 8 9
NM_001033559.1
NM_13081.2
EXON1
2 3 4 5 6 7 8 9
EXON1
2 3 4 5 6 7 8 9
EXON1
2 3 4 5 6 7 9
NEW
TR
AN
SC
RIP
TS
EXON1
2 3 4 5 6 7 9
V1
V1-1
V2
V3
V1-2
V1-3
V1-4
7’
8’
8’
S AS
S AS
M HU CH GO OR GI JM RH NM SQ CM
799 bp
1. Sin HS, Huh JW, Kim DS, Kang DW, Min DS, Kim TH, Ha HS, Kim HH, Lee SY, Kim HS. (2006) Transcriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells. Arch Virol. 151(10):1985-94.
2. Okahara G, Matsubara S, Oda T, Sugimoto J, Jinno Y, Kanaya F. (2004) Expression analyses of human endogenous retroviruses (HERVs): tissue-specific and developmental stage-dependent expression of HERVs. Genomics. 84(6):982-90
References
V1
V1-3
V1-4
V1-1,V1-2
GAPDH 120 bp
GAPDH 120 bp
V3
V2
Number 1 2 3 4 5 6 7 8
Tissues adrenal gland cerebellum heart kidney liver lung testis trachea
Hu
man
Inte
rgat
ion
Tim
e
LTR in CDS
0.01
7196
42
100 56
DYX1C1 HUDYX1C1 CH
DYX1C1 GODYX1C1 GI
100
DYX1C1 JMDYX1C1 RH
DYX1C1 CM
DYX1C1 SQDYX1C1 NM
LTR7
M 1 2 3 4 5 6 7 8 M 1 2 3 4 5 6 7 8
GAPDH 120 bp
V1
V1-3
V1-4
V1-1,V1-2
GAPDH 120 bp
V3
V2
Mod
el f
or D
YX
1C1
gen
e ev
olu
tion
Rh
esu
s
Coding region Untranslated regionLTR7
M 1 2 3 4 5 6 7 8 M 1 2 3 4 5 6 7 8
Retroelement
Retroposon
SINE
Retrotransposon
LINE
RNA intermediate
- LTR element + LTR element
- env + env
- RT + RT
Yeast Ty1/copia/truncated HERVsLTR ORF1 ORF2 LTR
LTR LTR
Human THE1
PPoly(A)
Human Alu
ORF1 ORF2PPoly(A)L1
Retrovirusgag pol envLTR LTR
Full-length HERVs/exogenous retrovirus
Human
Common ancestor
Rodents ancestor
Primate ancestor
Mouse RatNew World
monkeyOld World
monkey
LTR 7
PB1D9
B1F
Tandem duplication
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