Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.

Détails

ID Serval
serval:BIB_C0A73F212EB6
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.
Périodique
Journal of Molecular Biology
Auteur(s)
Roulet E., Bucher P., Schneider R., Wingender E., Dusserre Y., Werner T., Mermod N.
ISSN
0022-2836[print], 0022-2836[linking]
Statut éditorial
Publié
Date de publication
2000
Volume
297
Numéro
4
Pages
833-848
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Résumé
Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-specific DNA-binding of a transcription factor belonging to the CTF/NFI family. Using a systematic collection of rationally designed oligonucleotides combined with an in vitro DNA binding assay, we found that the sequence specificity of this protein cannot be represented by a simple consensus sequence or weight matrix. For instance, CTF/NFI uses a flexible DNA binding mode that allows for variations of the binding site length. From the experimental data, we derived a novel prediction method using a generalised profile as a binding site predictor. Experimental evaluation of the generalised profile indicated that it accurately predicts the binding affinity of the transcription factor to natural or synthetic DNA sequences. Furthermore, the in vitro measured binding affinities of a subset of oligonucleotides were found to correlate with their transcriptional activities in transfected cells. The combined computational-experimental approach exemplified in this work thus resulted in an accurate prediction method for CTF/NFI binding sites potentially functioning as regulatory regions in vivo.
Mots-clé
Adenoviruses, Human/genetics, Algorithms, Base Sequence, Binding Sites, CCAAT-Enhancer-Binding Proteins, Cell Line, Computer Simulation, Consensus Sequence/genetics, DNA/genetics, DNA/metabolism, DNA-Binding Proteins/metabolism, Dimerization, Humans, Mutation/genetics, NFI Transcription Factors, Oligodeoxyribonucleotides/chemistry, Oligodeoxyribonucleotides/genetics, Promoter Regions, Genetic/genetics, Replication Origin/genetics, Reproducibility of Results, Response Elements/genetics, Substrate Specificity, Thermodynamics, Transcription Factors/metabolism, Transcriptional Activation/genetics, Transfection
Pubmed
Web of science
Création de la notice
24/01/2008 10:41
Dernière modification de la notice
20/08/2019 15:35
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