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Janissen, R. (author), Barth, R. (author), Polinder, M.L. (author), van der Torre, J. (author), Dekker, C. (author)Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation of genetic processes in all domains of life. It has become common knowledge that, during transcription, the DNA-dependent RNA polymerase (RNAP) induces positive supercoiling ahead of it (downstream) and negative supercoils in its wake ...journal article 2024
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Agam, Ganesh (author), Barth, A. (author), Lamb, Don C. (author)It is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of...journal article 2024
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Barth, R. (author), Pradhan, B. (author), Kim, E. (author), Davidson, Iain F. (author), van der Torre, J. (author), Peters, Jan‑Michael ‑M (author), Dekker, C. (author)Correction to: Scientific Reports, published online 19 May 2023 The original version of this Article contained an error in Figure 1b-1, where the fore- and background order of the strands “DNA” (in black) and “Brn1 Kleisin” (in green), were switched. The original Figure 1 and accompanying legend appear below. (Figure presented.) Description...journal article 2023
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Tišma, M. (author), Janissen, R. (author), Antar, Hammam (author), Martin Gonzalez, A. (author), Barth, R. (author), Beekman, T.G.T. (author), van der Torre, J. (author), Michieletto, Davide (author), Gruber, Stephan (author), Dekker, C. (author)In most bacteria, chromosome segregation is driven by the ParABS system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex for Bacillus subtilis ParB, using single-molecule fluorescence microscopy and AFM imaging to show that...journal article 2023
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Davidson, Iain F. (author), Barth, R. (author), Zaczek, Maciej (author), van der Torre, J. (author), Tang, Wen (author), Nagasaka, Kota (author), Janissen, R. (author), Kerssemakers, J.W.J. (author), Wutz, Gordana (author), Dekker, C. (author), Peters, Jan Michael (author)In eukaryotes, genomic DNA is extruded into loops by cohesin<sup>1</sup>. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)<sup>2,3</sup> that have important roles in gene regulation and recombination during development and disease<sup>1,4–7</sup>. How CTCF...journal article 2023
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Yang, Sora (author), Klughammer, N. (author), Barth, A. (author), Tanenbaum, M. (author), Dekker, C. (author)Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic...journal article 2023
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Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have...review 2023
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Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical NanoporesKlughammer, N. (author), Barth, A. (author), Dekker, Maurice (author), Fragasso, A. (author), Onck, Patrick R. (author)The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single...journal article 2023
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De Franceschi, N. (author), Barth, R. (author), Meindlhumer, S. (author), Fragasso, A. (author), Dekker, C. (author)Membrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division and in other cellular processes such as endocytosis, virus release or bacterial sporulation. However, its mechanism remains poorly understood, impeding its application as a cell-division...journal article 2023
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Tous, Loic (author), Govaert, Jonathan (author), Harrison, Samuel (author), Carrière, Carolyn (author), Barth, Vincent (author), Giglia, Valentin (author), Buchholz, Florian (author), Chen, N. (author), Gordon, I.M.F. (author)The EU crystalline silicon (c-Si) PV manufacturing industry has faced strong foreign competition in the last decade. To strive in this competitive environment and differentiate itself from the competition, the EU c-Si PV manufacturing industry needs to (1) focus on highly performing c-Si PV technologies, (2) include sustainability by design,...journal article 2023
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Ploetz, Evelyn (author), Ambrose, Benjamin (author), Barth, A. (author), Börner, Richard (author), Kapanidis, Achillefs N. (author), Lohman, Timothy M. (author), Steffen, Fabio D. (author), Cordes, Thorben (author), Magennis, Steven W. (author), Lerner, Eitan (author)PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is...review 2023
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Barth, R. (author), Pradhan, B. (author), Kim, E. (author), Davidson, Iain F. (author), van der Torre, J. (author), Peters, Jan Michael (author), Dekker, C. (author)DNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated. The ring-like structure of SMC complexes prompted multiple models where the extruded DNA is topologically or...journal article 2023
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Tišma, M. (author), Panoukidou, Maria (author), Antar, Hammam (author), Soh, Young Min (author), Barth, R. (author), Pradhan, B. (author), Barth, A. (author), van der Torre, J. (author), Dekker, C. (author)The ParABS system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzzling how this large-distance spreading can occur along DNA loaded with hundreds of proteins. Using in...journal article 2022
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- Barth, Stephan (author), Carlson, Ola (author), Carroll, James (author), Kariniotakis, Georges (author), Kolios, Athanasios (author), Mann, Jakob (author), Muskulus, Michael (author), Watson, S.J. (author) contribution to periodical 2022
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Pradhan, B. (author), Barth, R. (author), Kim, E. (author), van Laar, T. (author), Yang, W.W.W. (author), Ryu, J.K. (author), van der Torre, J. (author), Peters, Jan Michael (author), Dekker, C. (author)Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no...journal article 2022
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Barth, R. (author), Shaban, Haitham A. (author)Gene transcription by RNA polymerase II (RNAPol II) is a tightly regulated process in the genomic, temporal, and spatial context. Recently, we have shown that chromatin exhibits spatially coherently moving regions over the entire nucleus, which is enhanced by transcription. Yet, it remains unclear how the mobility of RNA Pol II molecules is...journal article 2022
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Lerner, Eitan (author), Barth, A. (author), Hendrix, Jelle (author), Ambrose, Benjamin (author), Birkedal, Victoria (author), Blanchard, Scott C. (author), Börner, Richard (author), Joo, C. (author), Lee, Tae Hee (author)Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever- increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs...review 2021
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Li, M. (author), McDonald, B. C. (author), McKeen, S. A. (author), Eskes, H. (author), Levelt, Pieternel Felicitas (author), Francoeur, C. (author), Harkins, C. (author), He, J. (author), Barth, M. (author)Nitrogen oxides (NO<sub>x</sub>) are air pollutants critical to ozone and fine particle production in the troposphere. Here, we present fuel-based emission inventories updated to 2018, including for mobile source engines using the Fuel-based Inventory of Vehicle Emissions (FIVEs) and oil and gas production using the Fuel-based Oil and Gas ...journal article 2021
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Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcriptionShaban, Haitham A. (author), Barth, R. (author), Bystricky, Kerstin (author)The eukaryotic genome is hierarchically structured yet highly dynamic. Regulating transcription in this environment demands a high level of coordination to permit many proteins to interact with chromatin fiber at appropriate sites in a timely manner. We describe how recent advances in quantitative imaging techniques overcome caveats of...review 2020
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Barth, R. (author), Fourel, Genevieve (author), Shaban, Haitham A. (author)Chromatin ‘blobs’ were recently identified by live super-resolution imaging of labeled nucleosomes as pervasive but fleeting structural entities. However, the mechanisms leading to the formation of these blobs and their functional implications are unknown. We explore here whether causal relationships exist between parameters that characterize...journal article 2020
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