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Lesson from the SFTPB gene: evolutionary mechanism of exonization, Alu recombination-mediated deletion (ARMD), and alternative splicing could be occurred more frequently in diverse primate lineage. - PowerPoint PPT Presentation
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AbstractThe SFTPB (surfactant, pulmonary-associated protein B)
gene on human chromosome 2p11.2 encodes an amphipathic surfactant protein essential for lung function and homeostasis after birth. The SFTPB gene has been investigated to have transcript variants related with transposable elements (LTR7B and AluSx). We investigated the evolutionary aspect and molecular characterization of SFTPB gene using genomic DNAs and RNAs from various primate samples. LTR7B and AluSx elements within the SFTPB gene have been integrated into ancestor genome before the divergence of simian and prosimian. Alu recombination-mediated deletion (ARMD) event has been occurred after the divergence of New World monkeys and Old World monkeys in SFTPB gene 3’ UTR region. Transcript variants (306 bp and 463 bp) were newly identified by comparative RT-PCR analysis. Original transcript (419 bp) shows ubiquitous expression in various tissues and TE fusion transcript (841 bp) shows the lung specific expression in human. Taken together, integration event of LTR7B and AluSx on SFTPB gene seem to cause a lineage specific exonization event via general exonization event (New World monkeys and prosimian), ARMD event (Old World monkeys and hominoids), and alternative splicing (human) during the primate evolution. …………………….
Ja-Rang Lee1, Jae-Won Huh1,2, Dae-Soo Kim3, Hong-Seok Ha1, Kung Ahn1, Yun-Ji Kim1, Kyu-Tae Chang2, and Heui-Soo Kim1,*
1 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea2 National Primate Research Center (NPRC), KRIBB, Ochang, Chungbuk 363-883, Republic of Korea
3 Korea Bioinformation Center, KRIBB, Daejeon 305-806, Korea
1. Han, K., Lee J., Meyer, T. J., Wang, J., Sen, S. K., Srikanta, D., Liang, P. & Batzer, M. A. (2007). Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet. 3, 1939-1949.
2. Clark JC, Wert SE, Bachurski CJ, Stahlman MT, Stripp BR, Weaver TE, Whitsett JA. 1995. Targeted disruption of the surfactant protein B gene disrupts surfactant homeostasis, causing respiratory failure in newborn mice. Proc. Natl. Acad. Sci. USA. 92: 7794-7798.
References
Materials & Methods
BioinformaticsBioinformatics
Genomic DNA Genomic DNA & cDNA& cDNA
RT-PCRRT-PCRHuman, Rhesus monkey & Marmoset(30 cycle)
; Various tissues
PCR & Cloning PCR & Cloning of PCR productof PCR product
30 cycle; 94 - 40 sec, 56 - 30 sec, 72 - 40 ℃ ℃ ℃
sec
Qiaquick Gel-extraction, Promega T-easy Vector,
EcoR-I(DH5α)
http://www.primate.or.kr/HESAS/
Genomic DNA of various primate and human
cDNA of various tissues of human, rhesus
monkey & marmoset
IntroductionOther region
16%
Gene-related Sequence
36%
LINE
20%
SINE
13%
Cod
ing
sequ
ence
3%
Pseu
doge
ne
1%
HERV element
8%
DNA ele
men
t
3%
Results & DiscussionChr. 2
1 2 11_A10NM_198843.1 638 bpS
1AS2
1 2 10NM_000542.2
11_B
2p11.2
SFTPB Gene
Structure
638 bpS1
AS2
SFTPB Gene Expression in Various Tissues of Human
841 bp
306 bp
G3PDH 120 bp
Ad
ren
al g
lan
d
Bon
e m
arro
w
Cer
ebel
lum
Wh
ole
bra
in
Fet
al b
rain
Fet
al li
ver
Hea
rt
Kid
ney
Mar
ker
Liv
er
Lu
ng
Pla
cen
ta
Mar
ker
Tes
tis
Th
ymu
s
Pro
stat
e
Sal
ivar
y gl
and
Th
yroi
d
Ute
rus
Tra
chea
Sk
elet
al m
usc
le
Sp
inal
cor
d
Ad
ren
al g
lan
d
Bon
e m
arro
w
Cer
ebel
lum
Wh
ole
bra
in
Fet
al b
rain
Fet
al li
ver
Hea
rt
Kid
ney
Mar
ker
Liv
er
Lu
ng
Pla
cen
ta
Mar
ker
Tes
tis
Th
ymu
s
Pro
stat
e
Sal
ivar
y gl
and
Th
yroi
d
Ute
rus
Tra
chea
Sk
elet
al m
usc
le
Sp
inal
cor
d
419 bp
G3PDH 120 bp
841 bpS AS
NM_198843.1
New Transcript
NM_000542.2
New Transcript
419 bpS AS
463 bp
Cer
ebel
lum
Cer
ebru
m
Sto
mac
h
Pan
crea
s
Ad
ren
al g
lan
d
Hea
rt
Kid
ney
Liv
er
Lu
ng
Tes
tis
Mar
ker
Tra
chea
Sp
leen
Cec
um
Mar
ker
Rec
tum
Uri
ne
bla
dd
er
Gu
llet
Du
oden
um
Ton
gue
Jeju
nu
m
Sal
ivar
y gl
and
Col
on
Ileu
m
306 bp
G3PDH 120 bp
Ad
ren
al g
lan
d
Cer
ebel
lum
Cer
ebru
m
Hea
rt
Kid
ney
Liv
er
Lu
ng
Tes
tis
Mar
ker
Tra
chea
Sp
leen
Cec
um
Mar
ker
Rec
tum
Uri
ne
bla
dd
er
Gu
llet
Sto
mac
h
Du
oden
um
Ton
gue
Jeju
nu
m
Pan
crea
s
Sal
ivar
y gl
and
Col
on
Ileu
mG3PDH 120 bp
463 bp
SFTPB Gene Expression in Various Tissues of Rhesus monkey
419 bp
SFTPB Gene Expression in Various Tissues of New World monkeys
Mar
ker
Bra
in
Hea
rt
Kid
ney
Liv
er
Lu
ng
Mar
ker
Cer
ebel
lum
Hea
rt
Kid
ney
Lu
ng
Ute
rus
306 bp
G3PDH 120 bp
306 bp
G3PDH 120 bp
Mar
ker
Cer
ebel
lum
Hea
rt
Kid
ney
Liv
er
Lu
ng
Cer
ebel
lum
Hea
rt
Kid
ney
Lu
ng
Ute
rus
Mar
ker
G3PDH 120 bp
463 bp
419 bp
G3PDH 120 bp
638 bp
HU
CH
GO
OR
GI
JM RH
NMMar
ker
TA
RL
392 bp
HU
CH
GO
OR
GI
JM RH
NMMar
ker
TA
RL
763 bp
ARMD event and evolutionary aspect of the SFTPB gene
Integration lineage of HERV-H LTR and AluSx in the SFTPB gene
ARMD event
AluSg vs AluSx AluSxAluJ LTR7B?
AluSg AluSxAluJ LTR7B
Insertion of TEsInsertion of TEs
ARMD event
Alternative splicing
