Alu

1. Alu Alu J AluJb AluJo Alu S Alu Sx Alu Sg Alu Sp Alu Sc Alu Sq Alu Y

2. Alu elements contain many binding sites for transcription factors and may play a role in regulation of debelopmental processes BMC Genomics 2006, 7:133

3. Feature of Alus 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

4. The idea of Alu acting as a carrier of cis regularoty elements was suggested by Britten ; Evolutionary selection against change in many Alu repeat sequences 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

11. Alu elements within human mRNAs are probable microRNA targets TRENDS in Genetics Four microRNAs complementarity with MIR/LINE-2 elements At least some Alu elements within human mRNAs serve as microRNA targets

13. 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 Alu that is hit by the 6-mer core sequence (AAGUGC).

14. 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

15. Human Genomic Deletions Mediated by Recombination between Alu Elements The Americal Journal of Human Genetics Volume 79 july 2006

20. Lab application • 기존의 실험 모델을 Alu에 적용 – Alu의 promoter 로서의 역할. • 여러가지 경우의 다양한 Disscusion이 가능. 2. miRNA의 target이 되는 서열의 확인을 통해 Alu가 포함되어 있는 전사체의 운명 을 예측할 수 있으며 이를 질병에 적용시켜 실험에 응용할 수 있음 – polymorphis m 및 계통상에서의 연구 3. 논문에서 언급된 Alu를 통한 Recombination이 높은 homology를 가진 LTR서열 에서도 적용될 수 있을 것이며 계통상에서 보존된 유전자의 이상으로 인해 발생한 질병등에서 구조의 분석비교가 가능할 것이다.

21. 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

22. 8 RING-finger/IBR 1 2 3 4 5 6 7 8 9 10 11 AluJ MaLR Dorfin (RNF19) 1’ 2’ 3’ 4’ 5’ 6’ 7’ 8’ 9’ 10’ 8q22.2 AS1 S1 ORF S2 AS2

23. Skeletal muscle Adrenal gland Bone marrow Adult brain Cerebellum Spinal cord Fetal brain Fetal liver Placenta Trachea Prostate Thyroid Thymus Marker Marker Kidney Uterus Testis Heart Liver Lung Dorfin 494 bp 4 3 9 1 7 8 10 5 6 11 18 2 15 16 17 19 12 14 13 Gapdh 195 bp

24. (C) 1 2 3 11 AluJ MaLR 1) 1 2 10 AluJ MaLR 2) 1 2 11 3 AluJ MaLR 3) 115 bp 126 bp Primer S2 (A) (B) AGAAGCTGGAAGAGTCAAAGGACACATTCTCCCCTCAAGCCCCAGTGGGA AGAAGCTGGAAGAGTCAAAGGACACATTCTCCCCTCAAGCCCCAGTGGGA Breast (C) Breast (N) GCACGGCCCAGCTGGATTTTGGACTTCTGGCCTCCAGAACTAGACAGGGC Marker GCACGGCCCAGCTGGATTTTGGACTTCTGGCCTCCAGAACTAGACAGGGC CTCACTGTGTCACCCAGGGTGGAATACAGTGGTGTGATCATAGCTCACTG CTCACTGTGTCACCCAGGGTGGAATACAGTGGTGTGATCATAGCTCACTG AluJ element CAGCCTGGAATTCCTGGGCTCAAGCAACCCTGCCACCTCAGCCTTCCAAG CAGCCTGGAATTCCTGGGCTCAAGCAACCCTGCCACCTCAGCCTTCCAAG 1 556 bp TAGCTAGGACTACAGAACATCCATGATAGCAGTCTTCTGTAAATCGAACT TAGCTAGGACTACAGAACATCCATGATAGCAGTCTTCTGTAAATCGAACT 2 430 bp 3 315 bp TTTCAAGAATTCTCTGAAGGAACCAAGTAGGATATTCTTACATCATGACT TTTCAAGAATTCTCTGAAGGAACCAAGTAGGATATTCTTACATCATGACT G I I M E E E Q K Y N Q S F TAATGTGAATGCAAGAACAAGAAATAGGTTTTATCTCTAAATATAATGAA TAATGTGAATGCAAGAACAAGAAATAGGTTTTATCTCTAAATATAATGAA P I D G T S I V N L V S L L T C D GGGCTGTGTGTAAACACTGACCCTGTCTCAATTCTAACAAGCATTTTAGA GGGCTGTGTGTAAACACTGACCCTGTCTCAATTCTAACAAGCATTTTAGA Q R H R S D Q S S S L M D G L M CATGAGTTTACATCGGCAAATGGGTTCAGATCGAGATCTTCAGTCCTCTG CATGAGTTTACATCGGCAAATGGGTTCAGATCGAGATCTTCAGTCCTCTG M S L H R Q M G S D R D L Q S S A S S V S L P S V K K A P K K R R CTTCATCTGTGAGCTTGCCTTCAGTCAAAAAGGCACCCAAAAAAAGAAGA CTTCATCTGTGAGCTTGCCTTCAGTCAAAAAGGCACCCAAAAAAAGAAGA A S S V S L P S V K K A P K K R R R I S I G S L F R K K D N K R K S ATTTCAATAGGCTCCCTGTTTCGGAGGAAAAAAGATAACAAACGTAAATC ATTTCAATAGGCTCCCTGTTTCGGAGGAAAAAAGATAACAAACGTAAATC R I S I G S L F R K K D N K R K S R E L N G G V D G I A S I E S I AAGGGAGCTAAATGGCGGGGTGGATGGAATTGCAAGTATTGAAAGTATAC AAGGGAGCTAAATGGCGGGGTGGATGGAATTGCAAGTATTGAAAGTATAC R E L N G G V D G I A S I E S I Primer AS2

25. LTR-derived promoter transcript (556 bp) LTR-derived promoter transcript (430 bp) Relative Expression

26. Reverse Cos7 HCT116 Forward Reverse Forward Control 0 2 4 6 8 10 12 14 16 18 20 22 Relative Luciferase Activity (Fold of pGL-2 control)

27. CCCCACAAAA GATATGTTCA TGTCCTAATC CCCAGAATCT GCAAATGTTA TTTGGAAAAA GGGGTTTTGC AGATGTAATT AAGTTAAGAA TCTTGAGATAAGATCATCCT GGATTATCCA GGTAGCCTCA AAATCAAGTG ACAAGTGTCT TTGTAAGGGA CAAGTAGACC CATTACAGAG AAGACGACGC GCAGAAAAGG AGGAAGCAGT GTGCTCATGG AGGCGGAGAT TGGAGTGATG TAACCGCAAG CCGAGGAATG CTTATAGTCA CCAGAAGCTG GAAGAGTCAA AGGACACATT CTCCCCTCAA GCCCCAGTGG GAGCACGGCC CAGCTGGATT TTGGACTTCT GGCCTCCAGA ACTGTAAGAG AAATGTCCAT TGTCTTAAGC CAACCAGTTT GTGGTAGTTT GTTACAGCAG CCCCAGGAAA CTACTA . GATA-1 GATA-2 Nkx2-5 Nkx2-5 Whn ELF-1 +1 TRANSCRIPTION START SITE

28. 100 77 100 42 100 100