Presentaci

1
Finding conserved transcription factor binding
sites in promoter sequences
NfkappaB motifs in promoters controling human
NFkappaB gene family members
Markella Katidou Ulf Andersson Orom Carlos
Reguenga Filipe Vilas-Boas David Kuttenkeuler
2
The Project
The inhibitor of NFkappaB MAD3 in humans has been
shown to be regulated by NFkappaB itself.
Therefore we asked the question if other NFkappaB
family members are regulated in the same manner.
Approach Analysis of promoter sequences of six
NFkappaB family members in the human genome using
different web-based promoter analysis programs.
3
NFkappaB-Signaling
NFkappaB Dimer
Karin and Greten. Nature Immun. 2005
4

• Experimental identification of NFkB binding
  sites in MAD3 promoter (Le Bail, 1993).
• Therefore we decided to use 500bp of upstream
  sequence

5
Position of NFkB sites in the MAD3 family
upstream regions (500bp)
MAD3
NFKB1
C-Rel
RelB
NFKB2
RelA
TOUCAN workbench for regulatory sequence
analysis http//homes.esat.kuleuven.be/saerts/so
ftware/toucan.php
6
Control set of unrelated sequences (500bp)
Used our EMBO login numbers to find corresponding
NCBI gene IDS
Carlos adenosine A2b receptor Homo sapiens
David alcohol dehydrogenase 1C (class I), gamma
polypeptide Homo sapiens Ulf ADAM
metallopeptidase domain 10 Homo sapiens
Filipe poly (ADP-ribose) polymerase family,
member 4 Homo sapiens Markella adipose
differentiation-related protein Homo sapiens
7
TRES Transcription Regulatory Element Search a
tool for Comparative Promoter Analysis

• Uses TRANSFAC database, which contains 3980
  consensus transcription factor binding sites.
• multiple promoter sequence analysis with a
  maximum of 20 sequences at the same time.

http//bioportal.bic.nus.edu.sg/tres/
8
TRES output
MAD3 related sequences
control sequences
9
http//www.cbrc.jp/research/db/TFSEARCH.html
Maximum length 9,999bp analysis
10
(No Transcript)
11
Boxes that exist in all sequences
NFkappa-B family promoters
Control sequences
12
Boxes that exist in NFkappa-B promoters, but not
in the control promoters
GCF T00320 NFI/CTF T00094 p53 T00671
Pax-5 T00070 ENKTF-1 T00255 IRF-1 T00423
Sp1 T00759 NF-kappaB T00590 c-Jun T00133

Excluded short boxes with low score consensus
seuquence.
Included
Excluded
Pax5
NFkappa-B
13
oPOSSUM web tool
14
oPOSSUM output
15
Summary
We found NFkappaB sites in all human NFkappaB-
family gene promoters and not in the control set.
Therefore Web tools are usable to find specific
sites to a certain extent. A publication search
AFTER our analysis revealed this finding is true.
? (Bren et al. Oncogene 2001)