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The microarchitecture of DNA replication domains

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Abstract

Most DNA synthesis in HeLa cell nucleus is concentrated in discrete foci. These synthetic sites can be identified by electron microscopy after allowing permeabilized cells to elongate nascent DNA in the presence of biotin-dUTP. Biotin incorporated into nascent DNA can be then immunolabeled with gold particles. Two types of DNA synthetic sites/replication factories can be distinguished at ultrastructural level: (1) electron-dense structures—replication bodies (RB), and (2) focal replication sites with no distinct underlying structure—replication foci (RF). The protein composition of these synthetic sites was studied using double immunogold labeling. We have found that both structures contain (a) proteins involved in DNA replication (DNA polymerase α, PCNA), (b) regulators of the cell cycle (cyclin A, cdk2), and (c) RNA processing components like Sm and SS-B/La auto antigens, p80-coilin, hnRNPs A1 and C1/C2. However, at least four regulatory and structural proteins (Cdk1, cyclin B1, PML and lamin B1) differ in their presence in RB and RF. Moreover, in contrast to RF, RB have structural organization. For example, while DNA polymerase α, PCNA and hnRNP A1 were diffusely spread throughout RB, hnRNP C1/C2 was found only at the very outside. Surprisingly, RB contained only small amounts of DNA. In conclusion, synthetic sites of both types contain similar but not the same sets of proteins. RB, however, have more developed microarchitecture, apparently with specific functional zones. This data suggest possible differences in genome regions replicated by these two types of replication factories.

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Abbreviations

PCNA:

Proliferating cell nuclear antigen

GFP:

Green fluorescent protein

RB:

Replication bodies

RF:

Replication foci

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Acknowledgments

We thank Prof. Derenzini for advice on staining with osmium-ammine, Drs. M. Carmo-Fonseca, R. van Driel, I. Todorov, G. Dreyfuss, G. Blobel, Y. Raymond, and R.L. Ochs for kindly supplying antibodies, and Dr. J. Janáček for his help in the statistical evaluation of the results of colocalization experiments, and Dr. V. V. Philimonenko for critical reading of the manuscript. We thank BBSRC (Grant No. 36/G15592), the Grant Agency of the Academy of Sciences of the Czech Republic (Grant No. IAA5039202) and Ministry of Education, Youth and Sports (Grant No. LC 545). This work was also supported by the Institutional Grant No. AV0Z5039906.

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  1. Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Prague 4-Krč, Czech Republic

    Anatoly A. Philimonenko, Zdeněk Hodný & Pavel Hozák

  2. Faculty of Life Sciences, Jackson’s Mill, University of Manchester, Sackville Street, Manchester, M60 1QD, UK

    Dean A. Jackson

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  1. Anatoly A. Philimonenko
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Correspondence to Pavel Hozák.

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Philimonenko, A.A., Hodný, Z., Jackson, D.A. et al. The microarchitecture of DNA replication domains. Histochem Cell Biol 125, 103–117 (2006). https://doi.org/10.1007/s00418-005-0090-0

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