Transcription factors binding sites Group 2:
description
Transcript of Transcription factors binding sites Group 2:
Transcription factors binding sites Group 2:
Dora SapedeGustavo RezendeJennifer ZanetSalvatore D’AnielloShenqiu 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
E1 E2
3kb
3kb
singed gene Intron 1 = 12kbE3 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
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 CF2-II
TATATATATA TATATATATA
GENE ONTOLOGY
GO:Molecular function
DNA binding; RNA polymerase II transcription factor activity; transcription regulator activity; zinc ion binding; GO:Biologi
cal process
regulation of transcription, DNA-dependentGO:Cellular component
nucleus
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...
CF2= Chorion Transcription Factor
Data from Flybase :
Singed 3D Structure four singed domain
actin binding 1
actin binding 2