Laboratory of Cell Biology
The model of zipping loops.
Zipping of a DNA loop is shown. During replication, replisome couples produce a loop with the associated (zipped) arms probably in the form of four tightly associated 30 nm fibers. According to this model, ‘‘sister” pairs of biotin-dU-tagged segments of chromatids do not separate before the termination of the DNA synthesis of the replicon and the relaxation of the zipped arms. Immediately after labeling, the four tagged segments are present in one labeled domain (the left part of the image). Such an organization of the tagged segments persists during the synthesis of the whole replicon (the right part of the image). Although the mutual changes of the replisome position between the left and right parts of the Figure can result in the impression of movement of the replisome along the DNA, this model does not reflect whether the DNA or the replisome complex is moving during replication.
Two models of the arrangement of ‘‘sister” replisomes in HeLa cells and the effect of different organizations of biotin-dU-tagged segments on the number of labeled domains during various pulse-chase experiments.
The scheme shows the expected results of the consecutive mapping (indicated by arrows) of segments tagged during a short pulse of biotin-dUTP in the early S phase followed by chase periods of different lengths from the time immediately after the pulse (the upper part of the scheme) to the complete mitotic segregation of the sister chromatids (the lower part of the scheme).
3D reconstruction of the labeled domains.
The original image of a 200 nm-thick section of a cell nucleus is shown on the left (Scale bar: 500 nm), whereas a 3D reconstruction of the labeled domains reconstructed from the insert is shown on the right (Scale bar: 100 nm). The length measurement is demonstrated. The arrows indicate labeled domains traversing the section faces.
Current grants support
GA AS CR, KAN200520801, Targeted expression and transport of bioactive molecules, 2008–2012.
GA CR, 206/07/0233, Biochemical, ultrastructural and partial proteomic analysis of the penetration apparatus of bird Schistosoma cercariae, 2007–2010.
GA CR, 305/08/0535, Organization of human nuclear chromatin, 2009–2011.
GA AS CR, KJB500390701, Replication
of the mammalian genome – 4D view, 2007–2009.
of the mammalian genome – 4D view, 2007–2009.
Selected recent publications
1. Koberna K, Ligasová A, Malínský J, Pliss A, Siegel AJ, Cvačková Z, Fidlerová H, Mašata M, Fialová M, Raška I, Berezney R. (2005). Electron microscopy of DNA replication in 3-D: Evidence for similar-sized replication foci throughout S-phase. J Cell Biochem 94: 126–138.
2. Li J, Santoro R, Koberna K, Grummt I. (2005) the chromatin remodeling complex NoRC controls replication timing of rRNA genes. EMBO J 24: 120–127.
3. Stavreva DA, Kavasaki M, Dundr M, Koberna K, Muller WG, Tsujimura-Takahashi T, Komatsu W, Hayano T, Isobe T, Raška I, Misteli T, Takahashi N, McNally JG. (2006). Potential role for ubiquitin and the proteasome during ribosome biogenesis. Mol Cell Biol 26: 5131–5145. PDF file (2.0 MB)
4. Kalmárová M, Smirnov E, Mašata M, Koberna K, Ligasová A, Popov A, Raška I. (2007). Positioning of NORs and NOR-bearing chromosomes in relation to nucleoli. J Struct Biol 160: 49–56. PDF file (1.4 MB)
5. Ligasová A, Raška I, Koberna K. (2009) Organization of human replicon: singles or zipping couples. J Struct Biol 165: 204–213. PDF file (689 kB)
