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A biophysical model for transcription factories

Ana Z Canals-Hamann1, Ricardo Pires das Neves1, Joyce E Reittie1, Carlos Iñiguez2, Shamit Soneji1, Tariq Enver1, Veronica J Buckle1 and Francisco J Iborra13*

Author Affiliations

1 MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK

2 Departamento de Biotecnología, Universidad de Alicante, Alicante, 03080, Spain

3 Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología, CSIC, Darwin 3, Campus de Canto Blanco, Madrid, 28049, Spain

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BMC Biophysics 2013, 6:2  doi:10.1186/2046-1682-6-2

Published: 9 February 2013

Additional files

Additional file 1: Figure S1:

Stability of H4 K16Ac foci. Resistance of H4 K16Ac foci to various treatments that disrupted transcription or chromatin structure. The aspect of H4 K16Ac foci did not change after DRB treatment (2h 150 μM) or heat shock (Hs) for 1h at 45°C. Both treatments led to the release of RNA pol II from the genes. These foci were also resistant to NaCl extraction (cells permeabilised with 0.05% Triton X100 for 5 min in PBS at 4°C followed by 10 min extraction with 2M NaCl for 10 min). The images were pseudo-coloured for display. The bottom bar shows the scale of pseudo-colours used.

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Additional file 2: Figure S2:

H4 K16Ac foci are disassembled by formamide. The resistance of H4 K16Ac foci to formamide treatment. Cells were incubated for 5 min in PBS with different concentrations of formamide (0, 25, 50 and 100%) then fixed with 4% paraformaldehyde and immunolabelled with H4K16Ac antibodies. (a) The H4K16Ac foci were disassembled by formamide treatment, as can be seen from the change in the staining pattern, which is more diffuse and less intense than the control. The images were pseudo-coloured for display. (b) The deconstruction of the foci was quantified by the change in the pixel intensity variation coefficient (SD/mean). This analysis was performed by measuring the mean intensity and the standard deviation (SD) of the H4K16Ac signal of the nuclear areas in at least 200 cells for each treatment. The images were pseudo-coloured for display. The bottom bar shows the scale of pseudo-colours used.

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