A new way of looking at how the human genome folds to fit into the cell nucleus

12/22/2016

was developed by the Chromatin Systems Biology research Group of Dr. Argyris Papantonis at the CMMC, that allows for a new understanding of its structure-to-function relationship.

The way by which the 2-meter-long DNA fiber of human chromosomes is folded to fit into the cell nucleus (4 - 10 micrometer diameter) has been the epicenter of intense international research efforts over the last decade. The introduction of the “chromosome conformation capture” (3C) technology in 2002 has greatly advance our understanding of 3D genome folding. However, all 3C-based techniques used to address the aforementioned question rely on the chemical crosslinking of cells prior to their processing. Such a step carries inherent biases that may affect the quality and interpretation of results.

To overcome this issue, the research team led by Argyris Papantonis, a Junior Research Group at the Center for Molecular Medicine Cologne, developed a novel approach by which the three-dimensional architecture of human chromosomes can be interrogated in living cells without the need for chemical fixation.

In their recent work, published and highlighted in the latest issue of Molecular Systems Biology, a leading systems biology journal published by the European Molecular Biology Organization (EMBO), Dr. Papantonis and his colleagues introduced “intrinsic 3C” (i3C).

This new method offers unprecedented signal-to-noise ratios in the resulting chromatin interactions maps, and allows prominent features of chromatin folding to be readily identified against an ultra-low background. At the same time it outperforms existing methods and allows any biases of chemical fixation to be assessed and corrected for.

This interdisciplinary work brought together diverse expertise from three different campuses: molecular biology (Lilija Brant) and bioinformatics (Milos Nikolic, Theodore Georgomanolis) from the group of Dr. Papantonis at the CMMC, high throughput genomics (Frank Grosveld and Wilfred van Ijcken) from the Erasmus MC, as well as computational modeling (Chris Brackley and Davide Marenduzzo) from the University of Edinburgh. The i3C method and its analysis tools were applied to data generated in human primary cells and in mouse embryonic stem cells to illustrate their robustness and performance.

Now, the application of i3C will allow researchers (i) to forego any biases imposed by chemical crosslinking, (ii) to focus on direct and meaningful interactions between distant genomic fragments, and (iii) to study medically-relevant samples (e.g., tumour samples) that are typically very heterogeneous and of low cell counts. The team of Dr. Papantonis is currently using this approach to understand the changes imposed on the human genome under conditions of cellular senescence and premature ageing.

Original Publication
Brant L, Georgomanolis T, Nikolic M, Brackley CA, Kolovos P, van Ijcken W, Grosveld FG, Marenduzzo D, Papantonis A.
Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol Syst Biol (2016) 12: 891
doi: 10.15252/msb.20167311

For further information, please conctact:
Dr. Argyris Papantonis

Junior Group Leader in Systems Biology,
Center for Molecular Medicine, University of Cologne,
Robert Koch Str. 21, 50931 Cologne, Germany
E-mail: argyris.papantonis[at]uni-koeln.de
Phone: +49-221-478-96987

 

Argyris Papantonis and the members of his research team. (left to right: Costa Sofiadis, Theodore Georgomanolis, Lilija Brant, Argyris Papantonis (Head), Anne Zirkel, Milos Nikolic,)

Figure legend: The 3D folding of human chromosome 7 (ideogram) was investigated using the conventional (left) or the intrinsic Hi-C approach (right) and is displayed in 2D interactions heatmaps for the 1.5-Mbp region indicated (orange rectangle).