Journal ArticleDOI
Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization
Aleksandre Japaridze,Georgi Muskhelishvili,Georgi Muskhelishvili,Fabrizio Benedetti,Fabrizio Benedetti,Agni F. M. Gavriilidou,Renato Zenobi,Paolo De Los Rios,Paolo De Los Rios,Giovanni Longo,Giovanni Dietler +10 more
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TLDR
Very large supercoiled dsDNA is studied using high-resolution characterization, theoretical modeling, and molecular dynamics calculations to unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA-DNA interactions, which is called hyperplectonemes.Abstract:
Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understand the link between genetic regulation, DNA structure, and topology. Here, we study very large supercoiled dsDNA using high-resolution characterization, theoretical modeling, and molecular dynamics calculations. We unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA–DNA interactions, which we call hyperplectonemes. We demonstrate that their formation depends on DNA size, supercoiling, and bacterial physiology. We compare structural, nanomechanic, and dynamic properties of hyperplectonemes bound by three highly abundant nucleoid-associated proteins (FIS, H-NS, and HU). In all these cases, the negative supercoiling of DNA determines molecular dynamics, modulating their 3D shape. Overall, our findings provide a mech...read more
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Journal ArticleDOI
The condensin holocomplex cycles dynamically between open and collapsed states.
Je-Kyung Ryu,Allard J. Katan,Eli O. van der Sluis,Thomas Wisse,Ralph de Groot,Christian H. Haering,Cees Dekker +6 more
TL;DR: Atomic force microscopy shows that budding yeast condensin exhibits mainly open 'O' shapes and collapsed 'B' shapes, and it cycles dynamically between these two states over time, with ATP binding inducing the O to B transition.
Journal ArticleDOI
Direct imaging of the circular chromosome in a live bacterium.
Fabai Wu,Fabai Wu,Aleksandre Japaridze,Xuan Zheng,Jakub Wiktor,Jacob W. J. Kerssemakers,Cees Dekker +6 more
TL;DR: By quantitative time-lapse single-cell imaging of widened Escherichia coli cells, Wu and Japaridze et al. show that the circular chromosome exhibits a ring-like torus topology and a dynamic domain structure, providing an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells.
Journal ArticleDOI
Transcription of Bacterial Chromatin
Beth A. Shen,Robert Landick +1 more
TL;DR: Current understanding of transcription of bacterial chromatin is reviewed with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps, to anticipate answers that will define how bacterial Chromatin helps coordinate and dynamically regulate gene expression in changing environments.
Journal ArticleDOI
Chromosomal organization of transcription: in a nutshell
TL;DR: It is argued that the spatial organization of genome plays a fundamental role in its own regulation, in which activation of functionally relevant genes is coupled to and coordinated with the establishment of extended chromosomal domains of coherent transcription.
Journal ArticleDOI
Simultaneous orientation and 3D localization microscopy with a Vortex point spread function.
Christiaan N. Hulleman,Rasmus Ø. Thorsen,Eugene Kim,Cees Dekker,Sjoerd Stallinga,Bernd Rieger +5 more
TL;DR: In this paper, a Vortex point spread function was used to estimate the 3D position, dipole orientation, and degree of rotational constraint from a single 2D image, within 30% of the Cramer-Rao bound.
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