Alu Alu J AluJb

AluJo

Alu S Alu Sx

Alu Sg

Alu Sp

Alu Sc

Alu Sq

Alu Y

Alu elements contain many binding sites for transcription factors and may play a role in regulation of debelopmental processes

BMC Genomics 2006, 7:133

Distribution of Alu was found to be highly correlated with local GC content and with the density of genes and with intron density

Density of Alu is higher in intragenic(12.5% of the nucleotides) than in intergenic regions(9.6% of the nucleotides)

Alu elements are negatively selected in imprinted regions of primate genomes

Almost 20% of the genes contain transposable elements in the 3’UTR

Housekeeping genes contain more Alu than tissue specific genes

Feature of Alus

The idea of Alu acting as a carrier of cis regularoty elements was suggested by Britten ; Evolutionary selection against change in many Alu repeatsequences interspersed through primate genomes(1994)

Our findings show for the first time that TFs that are known to regulate the developmental processes may bind to Alu elements that are incorporated in the promoter regions of genes that need to be activated or suppressed during development

Alu elements within human mRNAs are probable microRNA targets

Four microRNAs complementarity with MIR/LINE-2 elements

At least some Alu elements within human mRNAs serve as microRNA targets

TRENDS in Genetics

Figure 3. The predicted RNA secondary structure of the Alu consensus sequence.The prediction was made using the Mfold server [18] (http://www.bioinfo.rpi.edu/applications/mfold/old/rna/). The bases in bold (GCACUU) indicate the site on Aluthat is hit by the 6-mer core sequence (AAGUGC).

There is no biological reason why Alu or other transposable elements within mRNAs should be regarded as unavailable for regulation by microRNAs

Indeed mRNAs that contain multiple Alu elements within their 3’UTRs should be regarded as particularly promising targets

Human Genomic Deletions Mediated by Recombination between Alu ElementsThe Americal Journal of Human Genetics Volume 79 july 2006

Lab application

1. 기존의 실험 모델을 Alu 에 적용 – Alu 의 promoter 로서의 역할 . 여러가지 경우의 다양한 Disscusion 이 가능 .

2. miRNA 의 target 이 되는 서열의 확인을 통해 Alu 가 포함되어 있는 전사체의 운명 을 예측할 수 있으며 이를 질병에 적용시켜 실험에 응용할 수 있음 – polymorphis m 및 계통상에서의 연구

3. 논문에서 언급된 Alu 를 통한 Recombination 이 높은 homology 를 가진 LTR 서열 에서도 적용될 수 있을 것이며 계통상에서 보존된 유전자의 이상으로 인해 발생한 질병등에서 구조의 분석비교가 가능할 것이다 .

이번 주 한 일

1. PERV promoter assay cloning 중

2. FPRL DSO control 잡았음

3. 홍콩 및 생명과학회 초록등록 완료

다음 주 할 일

1. 전체 조직에서의 FPRL2 realtime 실험

2. MOBP DSO control 잡기 및 전체 조직에서의 실험

3. 홈페이지 업뎃

8

MaLR

1’ 2’ 3’ 4’ 5’ 6’ 7’ 8’ 9’ 10’

3 4 5 6 7 8 9 10 111 2

AS2S2

Dorfin(RNF19)

AluJ

AS1S1

RING-finger/IBR

8q22.2ORF

Mar

ker

Ad

ren

al g

lan

d

Ad

ult

bra

in

Fet

al b

rain

Fet

al li

ver

Hea

rt

Kid

ney

Liv

er

Lu

ng

Bon

e m

arro

w

Cer

ebel

lum

Sk

elet

al m

usc

le

Mar

ker

Pla

cen

ta

Sp

inal

cor

d

Tes

tis

Th

ymu

s

Th

yroi

d

Tra

chea

Ute

rus

Pro

stat

e

Dorfin

Gapdh

494 bp

195 bp

1 4 5 6 7 8 9 102 3 1311 14 15 16 17 18 1912

Bre

ast

(N)

Bre

ast

(C)

Mar

ker

AAGGGAGCTAAATGGCGGGGTGGATGGAATTGCAAGTATTGAAAGTATAC

R LE GN G DV IG A

R LE GN G DV IG A IS

GCACGGCCCAGCTGGATTTTGGACTTCTGGCCTCCAGAACTAGACAGGGC

CTCACTGTGTCACCCAGGGTGGAATACAGTGGTGTGATCATAGCTCACTG

CAGCCTGGAATTCCTGGGCTCAAGCAACCCTGCCACCTCAGCCTTCCAAG

TAGCTAGGACTACAGAACATCCATGATAGCAGTCTTCTGTAAATCGAACT

TTTCAAGAATTCTCTGAAGGAACCAAGTAGGATATTCTTACATCATGACT

TAATGTGAATGCAAGAACAAGAAATAGGTTTTATCTCTAAATATAATGAA

GGGCTGTGTGTAAACACTGACCCTGTCTCAATTCTAACAAGCATTTTAGA

CATGAGTTTACATCGGCAAATGGGTTCAGATCGAGATCTTCAGTCCTCTG

CTTCATCTGTGAGCTTGCCTTCAGTCAAAAAGGCACCCAAAAAAAGAAGA

ATTTCAATAGGCTCCCTGTTTCGGAGGAAAAAAGATAACAAACGTAAATC

AAGGGAGCTAAATGGCGGGGTGGATGGAATTGCAAGTATTGAAAGTATAC

AGAAGCTGGAAGAGTCAAAGGACACATTCTCCCCTCAAGCCCCAGTGGGA

GCACGGCCCAGCTGGATTTTGGACTTCTGGCCTCCAGAACTAGACAGGGC

CTCACTGTGTCACCCAGGGTGGAATACAGTGGTGTGATCATAGCTCACTG

CAGCCTGGAATTCCTGGGCTCAAGCAACCCTGCCACCTCAGCCTTCCAAG

TAGCTAGGACTACAGAACATCCATGATAGCAGTCTTCTGTAAATCGAACT

TTTCAAGAATTCTCTGAAGGAACCAAGTAGGATATTCTTACATCATGACT

TAATGTGAATGCAAGAACAAGAAATAGGTTTTATCTCTAAATATAATGAA

GGGCTGTGTGTAAACACTGACCCTGTCTCAATTCTAACAAGCATTTTAGA

CATGAGTTTACATCGGCAAATGGGTTCAGATCGAGATCTTCAGTCCTCTG

CTTCATCTGTGAGCTTGCCTTCAGTCAAAAAGGCACCCAAAAAAAGAAGA

ATTTCAATAGGCTCCCTGTTTCGGAGGAAAAAAGATAACAAACGTAAATC

Primer S2

Primer AS2

M Q E Q E I G F S KI Y

G

N E

CL NV T PD SV I TL IS L D

M LS RH Q GM DS R LD SQ S

A SS SV L SP KV K PA KK R R

R SI GI S FL KR K ND RK K S

IS SE I

M LS RH Q GM DS R LD SQ S

A SS SV L SP KV K PA KK R R

R SI GI S FL KR K ND RK K S

SE I

AluJ element

AGAAGCTGGAAGAGTCAAAGGACACATTCTCCCCTCAAGCCCCAGTGGGA

556 bp430 bp315 bp

(A) (B)

(C)

3 111 2

MaLR AluJ

AluJMaLR

2 101

AluJMaLR

2 111 3

126 bp 115 bp

1)

2)

3)

123

0

0.005

0.01

0.015

0.02

0.025

0.03

0.035

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

LTR-derived promoter transcript (556 bp)

LTR-derived promoter transcript (430 bp)

Rel

ativ

e E

xpre

ssio

n

Reverse

Forward

Reverse

Forward

Control

Relative Luciferase Activity

(Fold of pGL-2 control)

0 2 4 6 8 10 12 14 16 18 20 22

Cos7

HCT116

CCCCACAAAA GATATGTTCA TGTCCTAATC CCCAGAATCT GCAAATGTTA TTTGGAAAAA GGGG

TTTTGC AGATGTAATT AAGTTAAGAA TCTTGAGATA AGATCATCCT GGATTATCCA GGTAGCCT

CA AAATCAAGTG ACAAGTGTCT TTGTAAGGGA CAAGTAGACC CATTACAGAG AAGACGACGC

GCAGAAAAGG AGGAAGCAGT GTGCTCATGG AGGCGGAGAT TGGAGTGATG TAACCGCAAG CC

GAGGAATG CTTATAGTCA CCAGAAGCTG GAAGAGTCAA AGGACACATT CTCCCCTCAA GCCCC

AGTGG GAGCACGGCC CAGCTGGATT TTGGACTTCT GGCCTCCAGA ACTGTAAGAG AAATGTCCA

T TGTCTTAAGC CAACCAGTTT GTGGTAGTTT GTTACAGCAG CCCCAGGAAA CTACTA

.

GATA-1

GATA-2

Nkx2-5 Nkx2-5

Whn ELF-1

+1 TRANSCRIPTION START SITE

Human

Dog

Pig

Cattle

Mouse

Rat

Chicken

Zebrafish

100

100

100

42

77

0.05

100

77

42

100

100

100

　 1 2 3 4 5 6 7 8

1. Human - 95.5 95.1 94.6 88.5 88.3 85.0 66.5

2. Dog 97.9 - 95.3 94.8 87.8 87.6 84.6 66.6

3. Pig 97.4 97.6 - 95.0 87.4 87.2 84.9 71.3

4.Ccattle 97.9 98.0 97.9 - 87.7 87.5 84.8 66.9

5. Mouse 93.6 93.1 92.7 93.5 - 93.6 83.8 68.0

6. Rat 92.9 92.3 92.1 92.6 96.4 - 82.9 73.0

7. Chicken 67.7 67.8 67.9 67.9 67.0 66.4 - 74.2

8. Zebrafish 51.5 51.8 51.8 51.6 51.4 51.8 51.6 - 　

　 　 　 　 　 　 　 　

dog pig cattle mouse rat chicken zebra fish　 　 　 　 　 　 　 　

Ka±SE 0.011 ± 0.003 0.014 ± 0.003 0.011 ± 0.003 0.032 ± 0.004 0.035 ± 0.004 0.027 ± 0.005 0.189 ± 0.013

Ks±SE 0.163 ± 0.015 0.166 ± 0.016 0.196 ± 0.016 0.387 ± 0.021 0.385 ± 0.022 0.566 ± 0.029 0.785 ± 0.027

Ka/Ks 0.067 0.084 0.056 0.083 0.091 0.048 0.241