1. Transcription factors binding sites Group 2: Dora Sapede Gustavo Rezende Jennifer Zanet Salvatore D’Aniello Shenqiu Wang

2. Promotor region analysis We have a DNA sequence and we want to find potential Transcription Factor (TF) binding sites ? ?

3. Strategies Use different programs to find potential TF binding sites Compare different results and choose TF(s) in common Relevance of TF in literature

4. E1E2 3kb singed gene Intron 1 = 12kb E3 E4 E5 hemocytes epidermis Looking for TFs binding to Singed Gene We searched a 3Kb region of the first intron, important for expression in epidermis

5. Programs used: Mat Inspector at http://www.genomatix.de/http://www.genomatix.de/ Transfac at http://www.cbrc.jp/research/db/TFSEARCH.htmlhttp://www.cbrc.jp/research/db/TFSEARCH.html Match at http://www.gene-regulation.com/pub/programs.html#matchhttp://www.gene-regulation.com/pub/programs.html#match Promo at http://alggen.lsi.upc.es/http://alggen.lsi.upc.es/ OTFBS at http://www.bioinfo.tsinghua.edu.cn/~zhengjsh/OTFBS/http://www.bioinfo.tsinghua.edu.cn/~zhengjsh/OTFBS/ To compare the results from different prediction tools

6. Mat Inspector:

7. Transfac:

8. Match:

9. Promo:

10. OTFB: (Over-represented Transcription Factor Binding Site Prediction Tool)

11. Positive control: Promoter region of even skipped; all 5 programs found hunchback sites!

12. Positive control: Promoter region of even skipped; all 5 programs found hunchback sites! TF binding sites programs results for fascin:

13. And… Mat Inspector, Transfac, OTFB: found in the region 1100 – 1120 a site for CF2-II TATATATATA

14. GENE ONTOLOGY GO:Molecular function DNA bindingDNA binding; RNA polymerase II transcription factor activity; transcription regulator activity; zinc ion binding; RNA polymerase II transcription factor activitytranscription regulator activityzinc ion binding GO:Biological process regulation of transcription, DNA-dependent GO:Cellular component nucleus EXPRESSION & PHENOTYPES Express ed in oogenesis, adult (egg chamber, follicle cell, ovary), adult, S (testis). details...egg chamberfollicle cellovarytestisdetails... Mutants affect denticle beltdenticle belt, dorsal appendage, egg chamber, embryonic/first instar larval cuticle, follicle cell. details...dorsal appendageegg chamber embryonic/first instar larval cuticlefollicle celldetails... CF2= Chorion Transcription Factor Data from Flybase :

15. Singed 3D Structure four singed domain actin binding 1 actin binding 2