000114878 001__ 114878
000114878 005__ 20190608070214.0
000114878 0247_ $$2doi$$a10.1006/jmbi.2000.3614
000114878 02470 $$2ISI$$a000086345700001
000114878 037__ $$aARTICLE
000114878 245__ $$aExperimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites
000114878 269__ $$a2000
000114878 260__ $$c2000
000114878 336__ $$aJournal Articles
000114878 500__ $$aLaboratory of Molecular Biotechnology, Centre for Biotechnology UNIL-EPFL and Institute of Animal Biology University of Lausanne, Lausanne, CH-1015, Switzerland.
000114878 520__ $$aAccurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-specific DNA-binding of a transcription factor belonging to the CTF/NFI family. Using a systematic collection of rationally designed oligonucleotides combined with an in vitro DNA binding assay, we found that the sequence specificity of this protein cannot be represented by a simple consensus sequence or weight matrix. For instance, CTF/NFI uses a flexible DNA binding mode that allows for variations of the binding site length. From the experimental data, we derived a novel prediction method using a generalised profile as a binding site predictor. Experimental evaluation of the generalised profile indicated that it accurately predicts the binding affinity of the transcription factor to natural or synthetic DNA sequences. Furthermore, the in vitro measured binding affinities of a subset of oligonucleotides were found to correlate with their transcriptional activities in transfected cells. The combined computational-experimental approach exemplified in this work thus resulted in an accurate prediction method for CTF/NFI binding sites potentially functioning as regulatory regions in vivo.
000114878 700__ $$aRoulet, E.
000114878 700__ $$0244404$$g113607$$aBucher, P.
000114878 700__ $$aSchneider, R.
000114878 700__ $$aWingender, E.
000114878 700__ $$aDusserre, Y.
000114878 700__ $$aWerner, T.
000114878 700__ $$aMermod, N.
000114878 773__ $$j297$$tJournal of Molecular Biology$$k4$$q833-48
000114878 909C0 $$xU11780$$0252244$$pGR-BUCHER
000114878 909CO $$pSV$$particle$$ooai:infoscience.tind.io:114878
000114878 937__ $$aGR-BUCHER-ARTICLE-2000-005
000114878 973__ $$rREVIEWED$$sPUBLISHED$$aOTHER
000114878 980__ $$aARTICLE