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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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slide1

Transcription factors binding sites Group 2:

Dora Sapede

Gustavo Rezende

Jennifer Zanet

Salvatore D’Aniello

Shenqiu Wang

slide2

Promotor region analysis

We have a DNA sequence and we want to find potential Transcription Factor (TF) binding sites

?

?

slide3

Strategies

Use different programs to find potential TF binding sites

Compare different results and choose TF(s) in common

Relevance of TF in literature

slide4

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

slide5

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

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OTFB:

(Over-represented Transcription Factor Binding Site Prediction Tool)

slide11

Positive control:

Promoter region of even skipped; all 5 programs found hunchback sites!

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Positive control:

Promoter region of even skipped; all 5 programs found hunchback sites!

TF binding sites programs results for fascin:

slide13

And…

Mat Inspector, Transfac, OTFB:

found in the region 1100 – 1120 a site for CF2-II

TATATATATA TATATATATA

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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...

slide15

Singed 3D Structure four singed domain

actin binding 1

actin binding 2