1. Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin
- Author
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Tatiana S. Karpova, James G. McNally, David A. Ball, Tatsuya Morisaki, Gunjan D. Mehta, Davide Mazza, Florian Mueller, Ronit Salomon-Kent, National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH), San Raffaele Scientific Institute, Vita-Salute San Raffaele University and Center for Translational Genomics and Bioinformatics, Colorado State University [Fort Collins] (CSU), Imagerie et Modélisation, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institute for Soft Matter and Functional Materials [Berlin], Helmholtz-Zentrum Berlin für Materialien und Energie GmbH (HZB), Intramural Research Program of National Institutes of Health (NIH), National Cancer Institute (NCI) and Center for Cancer Research (CCR). Funding for open access charge: Intramural Research Program of National Institutes of Health (NIH)., The authors would like to thank Dr Luke D. Lavis and Dr Jonatan B. Grimm (Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA) for JF HaloTag ligands. The authors acknowledge Euroscarf for providing pUG6 plasmid., Ball, Da, Mehta, Gd, Salomon-Kent, R, Mazza, D, Morisaki, T, Mueller, F, Mcnally, Jg, Karpova, Ts, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,Time Factors ,[SDV]Life Sciences [q-bio] ,dna ,MESH: Heat-Shock Proteins ,Genome ,Histones ,chemistry.chemical_compound ,MESH: Saccharomyces cerevisiae Proteins ,Heat-Shock Proteins ,transcription factor ,Genetics ,MESH: Histones ,MESH: Transcription Factors ,MESH: Saccharomyces cerevisiae ,Molecular Imaging ,Chromatin ,DNA-Binding Proteins ,Methods Online ,Inhouse research on structure dynamics and function of matter ,Saccharomyces cerevisiae Proteins ,Fluorophore ,Recombinant Fusion Proteins ,Saccharomyces cerevisiae ,yeasts ,Computational biology ,Biology ,MESH: Chromatin ,03 medical and health sciences ,MESH: Recombinant Fusion Proteins ,Transcription factor ,molecule ,MESH: Molecular Imaging ,MESH: Metallothionein ,MESH: Time Factors ,biology.organism_classification ,Yeast ,030104 developmental biology ,chemistry ,chromatin ,Metallothionein ,blinking ,DNA ,Function (biology) ,MESH: DNA-Binding Proteins ,Transcription Factors - Abstract
In vivo single molecule tracking has recently developed into a powerful technique for measuring and understanding the transient interactions of transcription factors (TF) with their chromatin response elements. However, this method still lacks a solid foundation for distinguishing between specific and non-specific interactions. To address this issue, we took advantage of the power of molecular genetics of yeast. Yeast TF Ace1p has only five specific sites in the genome and thus serves as a benchmark to distinguish specific from non-specific binding. Here, we show that the estimated residence time of the short-residence molecules is essentially the same for Hht1p, Ace1p and Hsf1p, equaling 0.12–0.32 s. These three DNA-binding proteins are very different in their structure, function and intracellular concentration. This suggests that (i) short-residence molecules are bound to DNA non-specifically, and (ii) that non-specific binding shares common characteristics between vastly different DNA-bound proteins and thus may have a common underlying mechanism. We develop new and robust procedure for evaluation of adverse effects of labeling, and new quantitative analysis procedures that significantly improve residence time measurements by accounting for fluorophore blinking. Our results provide a framework for the reliable performance and analysis of single molecule TF experiments in yeast.
- Published
- 2016
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