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699 results on '"Dekker, Cees"'

19. Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Author

Wu, Fabai, Swain, Pinaki, Kuijpers, Louis, Zheng, Xuan, Felter, Kevin, Guurink, Margot, Solari, Jacopo, Jun, Suckjoon, Shimizu, Thomas S, Chaudhuri, Debasish, Mulder, Bela, and Dekker, Cees

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Cell Cycle, Chromosome Segregation, Chromosomes, Bacterial, Escherichia coli, Molecular Dynamics Simulation, bacterial nucleoid, cell boundary confinement, chromosome segregation, chromosome size, crowders, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome.

Published
2019

31. Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points

Author

Nechemia-Arbely, Yael, Fachinetti, Daniele, Miga, Karen H, Sekulic, Nikolina, Soni, Gautam V, Kim, Dong Hyun, Wong, Adeline K, Lee, Ah Young, Nguyen, Kristen, Dekker, Cees, Ren, Bing, Black, Ben E, and Cleveland, Don W

Subjects
Human Genome, Genetics, Generic health relevance, Autoantigens, Cell Cycle, Cell Line, Tumor, Centromere, Centromere Protein A, Chromatin, Chromosomal Proteins, Non-Histone, DNA, DNA, Satellite, HeLa Cells, Histones, Humans, Nucleosomes, Hela Cells, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Chromatin assembled with centromere protein A (CENP-A) is the epigenetic mark of centromere identity. Using new reference models, we now identify sites of CENP-A and histone H3.1 binding within the megabase, α-satellite repeat-containing centromeres of 23 human chromosomes. The overwhelming majority (97%) of α-satellite DNA is found to be assembled with histone H3.1-containing nucleosomes with wrapped DNA termini. In both G1 and G2 cell cycle phases, the 2-4% of α-satellite assembled with CENP-A protects DNA lengths centered on 133 bp, consistent with octameric nucleosomes with DNA unwrapping at entry and exit. CENP-A chromatin is shown to contain equimolar amounts of CENP-A and histones H2A, H2B, and H4, with no H3. Solid-state nanopore analyses show it to be nucleosomal in size. Thus, in contrast to models for hemisomes that briefly transition to octameric nucleosomes at specific cell cycle points or heterotypic nucleosomes containing both CENP-A and histone H3, human CENP-A chromatin complexes are octameric nucleosomes with two molecules of CENP-A at all cell cycle phases.

Published
2017

32. Nanoscience and Nanotechnology Cross Borders.

Author

Khademhosseini, Ali, Chan, Warren WC, Chhowalla, Manish, Glotzer, Sharon C, Gogotsi, Yury, Hafner, Jason H, Hammond, Paula T, Hersam, Mark C, Javey, Ali, Kagan, Cherie R, Kotov, Nicholas A, Lee, Shuit-Tong, Li, Yan, Möhwald, Helmuth, Mulvaney, Paul A, Nel, Andre E, Parak, Wolfgang J, Penner, Reginald M, Rogach, Andrey L, Schaak, Raymond E, Stevens, Molly M, Wee, Andrew TS, Brinker, Jeffrey, Chen, Xiaoyuan, Chi, Lifeng, Crommie, Michael, Dekker, Cees, Farokhzad, Omid, Gerber, Christoph, Ginger, David S, Irvine, Darrell J, Kiessling, Laura L, Kostarelos, Kostas, Landes, Christy, Lee, Takhee, Leggett, Graham J, Liang, Xing-Jie, Liz-Marzán, Luis, Millstone, Jill, Odom, Teri W, Ozcan, Aydogan, Prato, Maurizio, Rao, CNR, Sailor, Michael J, Weiss, Emily, and Weiss, Paul S

Subjects
Nanoscience & Nanotechnology
Published
2017

33. The emerging landscape of single-molecule protein sequencing technologies

Author

Alfaro, Javier Antonio, Bohländer, Peggy, Dai, Mingjie, Filius, Mike, Howard, Cecil J., van Kooten, Xander F., Ohayon, Shilo, Pomorski, Adam, Schmid, Sonja, Aksimentiev, Aleksei, Anslyn, Eric V., Bedran, Georges, Cao, Chan, Chinappi, Mauro, Coyaud, Etienne, Dekker, Cees, Dittmar, Gunnar, Drachman, Nicholas, Eelkema, Rienk, Goodlett, David, Hentz, Sébastien, Kalathiya, Umesh, Kelleher, Neil L., Kelly, Ryan T., Kelman, Zvi, Kim, Sung Hyun, Kuster, Bernhard, Rodriguez-Larrea, David, Lindsay, Stuart, Maglia, Giovanni, Marcotte, Edward M., Marino, John P., Masselon, Christophe, Mayer, Michael, Samaras, Patroklos, Sarthak, Kumar, Sepiashvili, Lusia, Stein, Derek, Wanunu, Meni, Wilhelm, Mathias, Yin, Peng, Meller, Amit, and Joo, Chirlmin

Published
2021
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39. Towards a synthetic cell cycle

Author

Olivi, Lorenzo, Berger, Mareike, Creyghton, Ramon N. P., De Franceschi, Nicola, Dekker, Cees, Mulder, Bela M., Claassens, Nico J., ten Wolde, Pieter Rein, and van der Oost, John

Published
2021
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41. DNA-loop extruding condensin complexes can traverse one another

Author

Kim, Eugene, Kerssemakers, Jacob, Shaltiel, Indra A., Haering, Christian H., and Dekker, Cees

Subjects
DNA-ligand interactions -- Research, Genetic research, Adenosine triphosphatase -- Research, Molecular motors (Biochemistry) -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Condensin, a key component of the structure maintenance of chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA.sup.1. It remains unclear, however, how condensin complexes work together to collectively package DNA into chromosomes. Here we use time-lapse single-molecule visualization to study mutual interactions between two DNA-loop-extruding yeast condensins. We find that these motor proteins, which, individually, extrude DNA in one direction only are able to dynamically change each other's DNA loop sizes, even when far apart. When they are in close proximity, condensin complexes are able to traverse each other and form a loop structure, which we term a Z-loop--three double-stranded DNA helices aligned in parallel with one condensin at each edge. Z-loops can fill gaps left by single loops and can form symmetric dimer motors that pull in DNA from both sides. These findings indicate that condensin may achieve chromosomal compaction using a variety of looping structures. Single-molecule visualization shows that condensin--a motor protein that extrudes DNA in one direction only--can encounter and pass a second condensin molecule to form a new type of DNA loop that gathers DNA from both sides., Author(s): Eugene Kim [sup.1] , Jacob Kerssemakers [sup.1] , Indra A. Shaltiel [sup.2] , Christian H. Haering [sup.2] , Cees Dekker [sup.1] Author Affiliations: (1) Department of Bionanoscience, Kavli Institute [...]

Published
2020
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