Nucleosomes – Gatekeepers of the Genome?

In the cell nucleus the DNA is packaged into nucleosomes — complexes of a protein core with DNA wrapped around. Where these structures are positioned on the genome is a key factor for determining which genes are active and which genes are silenced. Wehave mapped for the first time the position of all nucleosomes in embryonic stem cells and compared these to cells that have developed further into specialized cell types. In the the next step we want to examine if nucleosome position changes are associated with cancer.

Embryonic stem cells can transform into any cell type of the body. They can become fibroblast cells as part of the skin or develop into neural cells in the brain. Yet, all the cells of an organism have essentially the same DNA sequence. How is it possible that their shapes and functions are so different? The key to this question is that depending on the type of cell only specific parts of the genetic program encoded in the DNA are being read and executed. The nucleosome – a complex of DNA wrapped around an octamer of proteins called histones – is thought to be the gatekeeper that decides what part of the genome is activated and what is locked away. On average, about 3/4 of the whole human genome is occluded by about 30 million nucleosomes that cover the almost 2 meters of DNA present in a human cell nucleus. Nucleosomes are arranged along the DNA like beads on the string. Thus, the positions of the nucleosomes can determine which parts of the DNA are free for contacts with other proteins that can read and interpret the genetic information.

Recent advancements in high-throughput DNA sequencing methods have made it possible to map all individual nucleosome positions in the genome at a single base-pair resolution. Taking advantage of this exciting new development and supported by the German Federal Ministry of Education and Research we have set out for an ambitious project: To map for the first time all nucleosome positions in mammalian embryonic stem cells in comparison to their differentiated counterparts, using mouse cells as a model system. In a collaboration with Thomas Höfer's group we identified features of nucleosome positioning at DNA sites that are important for cell differentiation: The start and the end of active genes had nucleosome-depleted regions in contrast to silent genes where these sites were covered with nucleosomes. Interestingly, the nucleosome positioning profiles were found to change according to specific modifications of the histone proteins with methyl and acetyl groups that can be attached and removed from the histones and represent so-called "epigenetic" signals. These signals are likely to direct energy-consuming molecular machines, the chromatin remodelers, to move nucleosomes along the DNA chain to another position.


Chain of nucleosomes with a protein binding to the linker DNA between nucleosomes (image courtesy of Gernot Längst).

As one would expect, many proteins that play a central role for cell development were found to bind to the free linker DNA between nucleosomes in embryonic stem cells, supporting the gatekeeper model for the role of nucleosomes in regulating DNA access. However, we were also in for a surprise: three of the master regulators of the stem cell state, the proteins Nanog, Oct4 and Sox2 were different. As Vladimir Teif, the first author of the study, puts it: "The nucleosome can't stop these proteins from binding to their DNA target site. They even might need the nucleosome to do their job".

The next step now is to elucidate how the process of active nucleosome translocation operates in the cell. In addition, we have already started extending our studies of nucleosome positioning and epigenetic modifications to cancer cells from patients with chronic lymphocytic leukemia. "We need to integrate the various epigenetic signals attached to the genome with changes of DNA access due to nucleosome repositioning" says Karsten Rippe. "This is crucial to understand how cells select their active genetic program and how this process is deregulated in cancer cells."

Teif, V. B., Vainshtein, Y., Caudron-Herger, M., Mallm, J.-P., Marth, C., Höfer, T. & Rippe, K. (2012). Genome-wide nucleosome positioning during embryonic stem cell development. Nat. Struct. Mol. Biol., published online 21 October 2012. doi: 10.1038/nsmb.2419 | Abstract | Reprint (7.4 MB)

The project was supported by the German Federal Ministry of Education and Research (BMBF) within the European EraSysBioPlus program.

German press release from the DKFZ

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