Finding conserved transcription factor binding sites in promoter sequences NfkappaB motifs in...
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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
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.
Karin and Greten. Nature Immun. 2005
NFkappaB-Signaling
NFkappaB Dimer
Experimental identification of NFkB binding sites in MAD3 promoter (Le Bail, 1993).
Therefore we decided to use 500bp of upstream sequence
Position of NFkB sites in the MAD3 family upstream regions (500bp)
TOUCAN: workbench for regulatory sequence analysis http://homes.esat.kuleuven.be/~saerts/software/toucan.php
MAD3NFKB1C-RelRelBNFKB2RelA
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]
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/
TRES output
MAD3 related sequences control sequences
http://www.cbrc.jp/research/db/TFSEARCH.html
Maximum length: 9,999bp analysis
NFkappa-B family promoters
Control sequences
Boxes that exist in all sequences
Excluded short boxes with low score consensus seuquence.
GCF [T00320]NFI/CTF [T00094] p53 [T00671] Pax-5 [T00070] ENKTF-1 [T00255] IRF-1 [T00423] Sp1 [T00759] NF-kappaB [T00590] c-Jun [T00133]
Boxes that exist in NFkappa-B promoters, but not in the control promoters
Included:
NFkappa-B Pax5
Excluded:
oPOSSUM web tool
oPOSSUM output
SummaryWe 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)
Program Advantage Disadvantage binding-site database used
TFSearch 10 kbp of sequence possible for analysis just one sequence to analyse TRANSFACPROMO multiple sequence analysis possible; fancy output;
many information. Filipe`s favouritethe output is a bit "unuebersichtlich"
TRANSFAC
TRES multiple sequence analysis possible; short clear output
not much additional information
TRANSFAC/ ooTFD/PLACE
oPOSSUM multiple sequence analysis possible; easy input (gene Ids), analysis of orthologous sequences
One cannot change sequence input
JASPAR
Toucan easy visualisation of multiple sequences promoter prediction is not working
TRANSFAC/ JASPAR