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Organization of the amplified type I interferon gene cluster and associated chromosome regions in the interphase nucleus of human osteosarcoma cells

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Abstract

The organization of the amplified type I interferon (IFN) gene cluster and surrounding chromosomal regions was studied in the interphase cell nucleus of the human osteosarcoma cell line MG63. Rather than being arranged in a linear ladder-like array as in mitotic chromosomes, a cluster of approximately 15 foci was detected that was preferentially associated along the periphery of both the cell nucleus and a chromosome territory containing components of chromosomes 4, 8, and 9. Interspersed within the IFN gene foci were corresponding foci derived from amplified centromere 4 and 9 sequences. Other copies of chromosomes 4 and 8 were frequently detected in pairs or higher-order arrays lacking discrete borders between the chromosomes. In contrast, while chromosomes 4 and 8 in normal WI38 human fibroblast and osteoblast cells were occasionally found to associate closely, discrete boundaries were always detected between the two. DNA replication timing of the IFN gene cluster in early- to mid-S phase of WI38 cells was conserved in the amplified IFN gene cluster of MG63. Quantitative RT-PCR demonstrated a ∼3-fold increase in IFNβ transcripts in MG63 compared with WI38 and RNA/DNA FISH experiments revealed 1–5 foci of IFNβ transcripts per cell with only approximately 5% of the cells showing foci within the highly amplified IFN gene cluster.

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Abbreviations

aCGH:

array comparative genomic hybridization

BAC:

bacterial artificial chromosome

CCD:

charge-coupled device

FISH:

fluorescent in situ hybridization

IFN:

interferon

PFA:

paraformaldehyde

poly(I:C):

polyriboinosinic:polyribocytidylic acid

SKY:

spectral karyotyping

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Acknowledgements

This work was supported by a grant from the National Institute of Health (GM-072131) to R. Berezney; grants LC535, MSM0021620806, and AV0Z50110509 to I. Raska; and the Excellence Initiative “REBIRTH”, the SFB 738, and the CliniGene Network of Excellence (European Commission FP6 Research Program, contract LSHB-CT-2006–018933) to J. Bode.

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Author notes

  1. Kishore S. Malyavantham

    Present address: Immco Diagnostics Inc., 60 Pineview Drive, Buffalo, NY, 14228, USA

  2. Sandra Goetze

    Present address: Center for Model Organism Proteomes, Institute of Molecular Biology, University of Zurich, Zurich, Switzerland

Authors and Affiliations

  1. Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA

    Michael J. Zeitz, Narasimharao V. Marella, Kishore S. Malyavantham & Ronald Berezney

  2. HZI, Helmholtz Centre for Infection Research/Epigenetic Regulation, Braunschweig, Germany

    Sandra Goetze & Juergen Bode

  3. Charles University in Prague, First Faculty of Medicine and Institute of Physiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic

    Ivan Raska

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  1. Michael J. Zeitz
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Correspondence to Ronald Berezney.

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Fig. S1

3D DNA FISH in human MG63 osteosarcoma and diploid HOB osteoblasts cells. (A, B) Regions of association between Chr4 red and Chr8 green in one MG63 cell, with corresponding line profiles. (C, D) Regions of association between Chr4 red and Chr8 green in two osteoblast cells, with corresponding line profiles (GIF 71.2 KB)

Fig. S1

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Zeitz, M.J., Marella, N.V., Malyavantham, K.S. et al. Organization of the amplified type I interferon gene cluster and associated chromosome regions in the interphase nucleus of human osteosarcoma cells. Chromosome Res 17, 305–319 (2009). https://doi.org/10.1007/s10577-009-9023-4

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