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Transcription factors binding sites Group 2:

Transcription factors binding sites Group 2:. Dora Sapede Gustavo Rezende Jennifer Zanet Salvatore D’Aniello Shenqiu Wang. Promotor region analysis. We have a DNA sequence and we want to find potential Transcription Factor (TF) binding sites. ?. ?. Strategies.

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Transcription factors binding sites Group 2:

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  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. We searched a 3Kb region of the first intron, important for expression in epidermis Looking for TFs binding to Singed Gene singed gene Intron 1 = 12kb E1 E2 E3 E4 E5 3kb 3kb hemocytes epidermis

  5. Programs used: Mat Inspector at http://www.genomatix.de/ Transfac at http://www.cbrc.jp/research/db/TFSEARCH.html Match at http://www.gene-regulation.com/pub/programs.html#match Promo at http://alggen.lsi.upc.es/ OTFBS at 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 TATATATATA

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

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

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