AbstractIntroduction Materials & Methods Results & Discussion PCR Electrophoresis Gel purification...
1
Abstract Introduction Materials & Methods Results & Discussion PCR Electrophoresis Gel purification Transformation1 Transformation2 Ligation Inoculation Plasmid DNA Isolation Gene Cloning References Genomic DNAs & cDNA PCR & RT-PCR Bioinformatics QIAEX II gel extraction k it(Qiagen) High Pure plasmid isolati on kit BLAST,MEGA3 Human , Monkeys Activation of HERV-H LTR in DYX1C1 gene during the primate evolution Yun-Ji Kim 1 , Jae-Won Huh 1 , Dae-Soo Kim 2 , Hong-Seok Ha 1 , Kung Ahn 1 , Ja-Rang Lee 1 , and Heui-Soo Kim 1, 2 1 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Ko rea 2 PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, B usan 609-735, Republic of Korea http://www..primate.or.kr Pseudogenes LTR LTR provirus LTR LTR Enodgenous retrovirus Exogenous Retroviruses Retrotransposons Endogenous Retroviruses budding proteins (gag, env) translation infection REVERSE TRANSCRIPTION transcription integration cDNA AAA mRNA AAA mRNA transcription LTR LTR re - integration translation proteins (gag, env) REVERSE TRANSCRIPTION cDNA Particle formation(budding) LTR LTR re - integration Particle formation no re-infection LTR LTR retrotransposon AAA transcription mRNA cDNA REVERSE TRANSCRIPTION Cellular gene pseudogene splicing AAA REVERSE TRANSCRIPTION cDNA integration transcription spliced- mRNA translation proteins (gag) Retroelement Retroposon SINE Retrotransposon Retrovirus LINE RNA intermediate - LTR element + LTR element - env + env - RT + RT Yeast Ty1/copia/truncated HERVs LTR ORF1 ORF2 LTR LTR LTR Human THE1 P Poly(A) Human Alu ORF1 ORF2 P Poly(A) L1 gag pol env LTR LTR Full-length HERVs/exogenous retrovirus 1.Sin HS, Huh JW, Kim DS, Kang DW, Min DS, Kim TH, Ha HS, Kim HH, Lee SY, Kim HS. (2006) Transcripti onal control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells. Arch V irol. 151(10):1985-94. 2. Okahara G, Matsubara S, Oda T, Sugimoto J, Jinno Y, Kanaya F. (2004) Expression analyses of huma n endogenous retroviruses (HERVs): tissue-specific and developmental stage-dependent expression of HERVs. Genomics. 84(6):982-90 DYX1C1 (dyslexia susceptibility 1 candidate 1) gene on human chromosome 15q21.3 is a candidate gene for developmental dyslexia. The DYX1C1 has three alternatively spliced transcripts. 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. The DYX1C1 gene was expressed in several human tissues with different spliced forms. It also showed similar expression patterns in various monkey tissues. Taken together, integration event of the HERV-H LTR element ………………...contributed to the transcript diversification of …………….......DYX1C1 during the primate evolution.………. Chr.1 5 q21.3 799b p M HU CH GO OR GI JM RH NM SQ CM LTR7 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 TRANSCRIPTS 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 V1 V1-3 V1-4 V1-1 V1-2 marke r adrenal gland cerebell um adult brain (whole) heart kidne y liver lung testi s trach ea bone marrow marke r fetal brain fetal liver placenta prost ate salivary gland sk-muscle spinal cord thymu s thyro id uteru s Human Rhesus marke r adrenal gland cerebell um adult brain (whole) heart kidne y liver lung testi s trach ea bone marrow marke r fetal brain fetal liver placenta prost ate salivary gland sk-muscle spinal cord thymu s thyro id uteru s V3 V2 cerebrum adrenal gland spleen marke r cerebell um heart kidne y liver lung testi s trach ea marke r colon cecum esophagu s stomach pancreas salivary gland rectum urine bladder duodenu m jejunum V1 V1-3 V1-4 V1-1 V1-2 marke r adrenal gland cerebell um cerebrum heart kidne y liver lung testi s trach ea marke r colon cecum esophagu s pancreas salivary gland rectum urine bladder duodenu m jejunum spleen stomach V3 V2 Coding region Untranslated re gion LTR7 DYX1C1 HU DYX1C1 CH DYX1C1 GO DYX1C1 GI DYX1C1 JM DYX1C1 RH DYX1C1 SQ DYX1C1 NM DYX1C1 CM 100 56 100 71 96 42 0.01
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Transcript of AbstractIntroduction Materials & Methods Results & Discussion PCR Electrophoresis Gel purification...
Abstract Introduction
Materials & Methods
Results & Discussion
PCR
Electrophoresis Gel purification
Transformation1
Transformation2
Ligation
Inoculation
Plasmid DNAIsolation
Gene Cloning
References
Genomic DNAs& cDNA
PCR & RT-PCR
Bioinformatics
QIAEX II gel extraction kit(Qiagen)High Pure plasmid isolation kit
BLAST,MEGA3
Human , Monkeys
Activation of HERV-H LTR in DYX1C1 gene during the primate evolution
Yun-Ji Kim1, Jae-Won Huh1, Dae-Soo Kim2, Hong-Seok Ha1, Kung Ahn1, Ja-Rang Lee1, and Heui-Soo Kim1, 2
1 Division 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
Pseudogenes
LTR LTR
provirus
LTR LTR
Enodgenous retrovirus
Exogenous Retroviruses
RetrotransposonsEndogenous Retroviruses
buddingproteins(gag, env)
translation
infection
REVERSE
TRANSCRIPTION
transcription
integrationcDNA
AAA
mRNA
AAA
mRNA transcription
LTR LTR
re - integration
translation
proteins(gag, env)
REVERSETRANSCRIPTION
cDNA
Particle formation(budding)
LTR LTR
re - integrationParticle formationno
re-infection
LTR LTR
retrotransposonAAAtranscription
mRNA
cDNA
REVERSETRANSCRIPTION
Cellular gene
pseudogene
splicing
AAA
REVERSETRANSCRIPTION
cDNAintegration
transcriptionspliced- mRNA
translation
proteins(gag)
Retroelement
Retroposon
SINE
Retrotransposon
RetrovirusLINE
RNA intermediate
- LTR element + LTR element
- env + env
- RT + RT
Yeast Ty1/copia/truncated HERVsLTR ORF1 ORF2 LTR
LTR LTR
Human THE1P
Poly(A)
Human Alu
ORF1 ORF2PPoly(A)L1
gag pol envLTR LTR
Full-length HERVs/exogenous retrovirus
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
DYX1C1 (dyslexia susceptibility 1 candidate 1) gene on human chromosome 15q21.3 is a candidate gene for developmental dyslexia. The DYX1C1 has three alternatively spliced transcripts. 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. The DYX1C1 gene was expressed in several human tissues with different spliced forms. It also showed similar expression patterns in various monkey tissues. Taken together, integration event of the HERV-H LTR element ………………...contributed to the transcript diversification of …………….......DYX1C1 during the primate evolution.……….
Chr.15
q21.3
799bp
M HU CH GO OR GI JM RH NM SQ CMLTR7
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
V1
V1-3
V1-4
V1-1 V1-2
mark
eradre
nal
gla
nd
cere
bellu
madult
bra
in
(whole
)heart
ki
dne
y liv
er
lung
test
istr
ach
eabone m
arr
ow
mark
erfe
tal
bra
infe
tal live
rpla
centa
pro
statesa
liva
ry
gla
nd
sk-m
uscle
spin
al
cordthym
usth
yro
idute
rus
Human Rhesus
mark
eradre
nal
gla
nd
cere
bellu
madult
bra
in
(whole
)heart
ki
dne
y liv
er
lung
test
istr
ach
eabone m
arr
ow
mark
erfe
tal
bra
infe
tal live
rpla
centa
pro
statesa
liva
ry
gla
nd
sk-m
uscle
spin
al
cordthym
usth
yro
idute
rus
V3
V2
cere
bru
m
adre
nal
gla
nd
sple
en
mark
er ce
rebellu
m heart
ki
dne
y liv
er
lung
test
istr
ach
ea m
ark
erco
lon
cecu
meso
phag
usst
om
ac
hpancr
eas
saliva
ry
gla
nd
rect
um
uri
ne
bla
dder
duoden
umje
junum
V1
V1-3
V1-4
V1-1 V1-2
mark
eradre
nal
gla
nd
cere
bellu
mce
rebru
mheart
ki
dne
y liv
er
lung
test
istr
ach
ea m
ark
erco
lon
cecu
meso
phag
us pancr
eas
saliva
ry
gla
nd
rect
um
uri
ne
bla
dder
duoden
umje
junum
sple
en
stom
ac
h
V3
V2
Coding region Untranslated region
LTR7
DYX1C1 HU
DYX1C1 CH
DYX1C1 GO
DYX1C1 GI
DYX1C1 JM
DYX1C1 RH
DYX1C1 SQ
DYX1C1 NM
DYX1C1 CM
100
56100
7196
42
0.01
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