Browsing by Author "Stamatov, Rumen"

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    A noisy linear map underlies oscillations in cell size and gene expression in bacteria.
    (Nature, 2015-07-16) Tanouchi, Yu; Pai, Anand; Park, Heungwon; Huang, Shuqiang; Stamatov, Rumen; Buchler, Nicolas E; You, Lingchong
    During bacterial growth, a cell approximately doubles in size before division, after which it splits into two daughter cells. This process is subjected to the inherent perturbations of cellular noise and thus requires regulation for cell-size homeostasis. The mechanisms underlying the control and dynamics of cell size remain poorly understood owing to the difficulty in sizing individual bacteria over long periods of time in a high-throughput manner. Here we measure and analyse long-term, single-cell growth and division across different Escherichia coli strains and growth conditions. We show that a subset of cells in a population exhibit transient oscillations in cell size with periods that stretch across several (more than ten) generations. Our analysis reveals that a simple law governing cell-size control-a noisy linear map-explains the origins of these cell-size oscillations across all strains. This noisy linear map implements a negative feedback on cell-size control: a cell with a larger initial size tends to divide earlier, whereas one with a smaller initial size tends to divide later. Combining simulations of cell growth and division with experimental data, we demonstrate that this noisy linear map generates transient oscillations, not just in cell size, but also in constitutive gene expression. Our work provides new insights into the dynamics of bacterial cell-size regulation with implications for the physiological processes involved.
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    Predicting In Vivo Transcription Factor Occupancy from In Vitro Binding
    (2014) Stamatov, Rumen

    The spatial pattern of transcription factor (TF) binding and the level of TF occupancy at individual sites across the genome determine how a TF regulates its targets. Consequently, predicting the location and level of TF binding genome-wide is of great importance and has received much attention recently. Protein-binding microarray (PBM) technology has become the golden standard for studying TF-DNA interactions in vitro, while Chromatin Immunoprecipitation followed by DNA Sequencing (ChIP-seq) is the standard method for inferring TF binding in vivo. However, direct interpretation of in vitro results in an in vivo context is challenging and to-date remains scarce. In this study, we focus on the E2F family of paralogous TFs, whose mode of binding to DNA has been controversial. Previous studies have shown that E2F factors bind to the TTTSSCGCG motif, where S can be a C or a G. Still, only a small fraction of in vivo targets are reported to contain this motif, hinting at indirect recruitment of the protein. We observed that genomic occupancy of E2F factors directly correlates with their in vitro binding affinities. By using data from universal PBM experiments, we show that E2F factors likely bind to DNA through direct sequence recognition and not through cofactor interaction. Furthermore, we developed a kinetic binding model using the PBM data to describe competition between different members of the E2F family and successfully distinguished between their unique targets. Overall, these results demonstrate how the straightforward and simple in vitro PBM experiments can be used for inferring the complex in vivo landscape of TF binding and elucidate the mechanism of E2F-DNA interaction.