Transcription factors binding sites Group 2 Dora Sapede
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 Use different programs to find potential TF binding sites Compare different results and choose TF(s) in common Relevance of TF in literature
Looking for TFs binding to Singed Gene singed gene Intron 1 = 12 kb E 1 E 2 E 3 E 4 E 5 3 kb hemocytes epidermis We searched a 3 Kb region of the first intron, important for expression in epidermis
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
Mat Inspector:
Transfac:
Match:
Promo:
OTFB: (Over-represented Transcription Factor Binding Site Prediction Tool)
Positive control: Promoter region of even skipped; all 5 programs found hunchback sites!
Positive control: Promoter region of even skipped; all 5 programs found hunchback sites! TF binding sites programs results for fascin:
And… Mat Inspector, Transfac, OTFB: found in the region 1100 – 1120 a site for CF 2 -II TATATATATA
CF 2= Chorion Transcription Factor Data from Flybase : GENE ONTOLOGY 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 EXPRESSION & PHENOTYPES Express ed 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. . .
Singed 3 D Structure four singed domain actin binding 1 actin binding 2
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