Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell

By S. Matsuoka, Bryan A. Ballif, Dong Zhang, Agata Smogorzewska, Steven P. Gygi, Stephen J. Elledge. Science, 2007

889 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/824ad6d7b6d09dc9b90384c5f87af186c696c903

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Citations in the corpus

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila (2012, positive): “coli cells, at any instant 20% of Lac I transcription factor molecules make functional contacts with target cis-regulatory DNA recognition sites, 10% are not bound to DNA, and 70% make low-occupancy, nonfunctional DNA interactions (13, 15).”
Intermittent search strategies (2011, positive): “Sliding phases have been clearly identified (both in vitro (Kabata et al., 1993) and in vivo (Bakk and Metzler, 2004; Elf et al., 2007; Wang et al., 2006)), as well as hopping/jumping phases (Bonnet et al., 2008; Gowers et al., 2005; Komazin-Meredith et al., 2008; van den Broek et al., 2008).”
Nonlinear optical signals and spectroscopy with quantum light (2016, neutral): “Possible in- coherent detection modes include fluorescence (Barkai, 2008; Elf et al., 2007), photoaccoustic (Patel and Tam, 1981), AFM (Mamin et al., 2005; Poggio et al., 2009; Rajapaksa and Kumar Wickramasinghe, 2011; Rajapaksa et al., 2010) or photocurrent detection (Cheng and Xie, 2012; Nardin…”
Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila (2014, neutral): “Transcription factors (TFs) are driven thermodynamically to bind to thousands of sites in genomic DNA, oftentimes nonspecifically (Lin and Riggs 1975; Walter et al. 1994; Phair et al. 2004; Elf et al. 2007; Zeitlinger et al. 2007; Li et al. 2008).”
How a protein searches for its site on DNA: the mechanism of facilitated diffusion (2009, neutral): “Consistent with this result most well-characterized proteins have been shown to slide sufficiently fast with σ ≈ 1–2kBT [21, 26, 29, 30, 34].”
Single-Cell and Single-Molecule Analysis of Gene Expression Regulation (2016, positive): “Although FCS and FRAP experiments measure the average movement of many molecules, super-resolution fluorescence microscopy allowed the development of SPT techniques for the quantification of TF dynamics with molecular resolution (29, 46, 73, 93).”
Time scale of diffusion in molecular and cellular biology (2014, positive): “The search can alternate between three-dimensional diffusion in the nucleus and one-dimensional diffusion along the DNA (figure 8) (Elf et al 2007, Wang et al 2006, Von Hippel and Berg 1989).”
DNA-binding specificities of human transcription factors. (2013, positive): “Furthermore, due to the fact that TFs can read the minor groove without opening the DNA, such interactions may also increase speed by which TFs locate their target sites (see Elf et al., 2007).”
Stochastic models of intracellular transport (2013, neutral): “On the other hand, single–molecule measurements indicate that D1 D3 (Elf et al., 2007; Yang et al., 2006).”