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