Defined structural changes occur in a nucleosome upon Amt1 transcription factor binding.
Here, we study the binding of the transcription factor Amt1 to its recognition site near the dyad of a highly positioned nucleosome. We find that the DNA binding domain of Amt1 binds to nucleosomes with only threefold reduced affinity compared to free DNA. We show by fluorescence resonance energy transfer that factor binding at the nucleosomal dyad is accompanied by the partial dissociation of the DNA ends from the histone octamer surface; however, no dissociation or subtle rearrangements of histone subunits is observed. A poly(dA.dT) DNA sequence element adjacent to the transcription factor binding site appears to facilitate factor binding, but is not essential. The methods that we describe here characterize for the first time the subtle structural changes that occur upon transcription factor binding to nucleosomes, and demonstrate the ability of the nucleosome to structurally adapt in response to outside influences.
White
Cindy L
CL
Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO-80523-1870, USA.
Luger
Karolin
K
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D003850:Deoxyribonuclease I / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D005656:Fungal Proteins; D006657:Histones / Q000378:metabolism*; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000378:metabolism*; D011067:Poly dA-dT; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D011487:Protein Conformation; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014982:Xenopus laevis / Q000378:metabolism
D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D006657:Histones; D009707:Nucleosomes; D014157:Transcription Factors; C069807:AMT1 protein, Candida glabrate; D011067:Poly dA-dT; D004247:DNA; D003850:Deoxyribonuclease I