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Nucleosomes and DNA methylation – the 'memory knots' of the cell?

 

All human cells have essentially the same DNA sequence in their genome. Yet their shape and properties are very different. Differences arise as only selected combinations of genes are expressed in a given cell type and wrong decisions during this process can lead to cancer. Thus, on top of the genetic information encoded in the DNA sequence an additional layer of so-called epigenetic marks exists that determines the active parts of the cell's genetic program. In a study headed by Vladimir Teif and published now in the August issue of Genome Research, we made progress to solve one of the many puzzles with respect to how epigenetic signals change the cell's genome organization and expression program during development.

Embryonic stem cells can transform into any cell type of the body by selecting specific parts of DNA sequence information common for all cells. They can, for example, become fibroblast cells as part of the skin or develop into neural cells in the brain. A complex network of epigenetic signals associated with the DNA sequence determines the active parts of the cell's genetic program. One well-established epigenetic mark is methylation of DNA cytosine residues. This epigenetic signal is reversible as DNA cytosine methylation can be removed via a change to hydroxymethylation. However, while several studies have shown that the DNA (hydroxy)methylation pattern is strikingly different between embryonic stem cells, normal differentiated cell and cancer cells, the functional consequences of changing the DNA methylation pattern are only partly understood. In particular, changes of gene activity and DNA methylation show little correlation in many cases.

An example of quipus, the ancient 'memory knots' or 'talking knots' used by the Incas for recording numbers and making simple calculations (source: "Manual of Writing in Quipus" by Miguel Angel Calvo Rodriguez).

Together with our colleagues we set out to resolve this puzzling finding. We followed the hypothesis that DNA methylation is linked with the positioning of nucleosomes in the genome. The nucleosome – a complex of DNA wrapped around a protein core in almost two turns – is thought to be the gatekeeper of the genome. Many transcription factors can bind much better to the linker DNA between nucleosomes, and thus their positioning can directly determine access to the genome. On average, about ¾ 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. Thus, throughout the genome, nucleosome position pattern can affect which parts of the DNA are free for contacts with other proteins that can read and interpret the genetic information. In analogy to the ancient quipus – the knots made into threads or strings by the Incas to record numbers – one could therefore consider the position of nucleosome to be 'memory knots' in the genome.

In our study we found that nucleosome positioning is linked with DNA methylation. At sites were DNA methylation was replaced by hydroxymethylation in stem cells the nucleosomes became unstable and were easily displaced by the CTCF DNA-binding protein. In previous studies, CTCF has been found to act both as a tumor suppressor and an oncogene and is considered to be the 'master weaver of the genome'. It has several thousands of binding sites in the genome and acts by making DNA loops to separate active and inactive parts of the DNA. Thus, by changing the DNA (hydroxy)methylation between embryonic stem cells and their differentiated counterparts the nucleosome position patterns and CTCF binding were changed. In turn this would lead to changes of the spatial organization of genome and the active gene expression program. As Vladimir Teif, the first author of the study, puts it: "Due to this linkage a DNA methylation signal largely increases its effective range. Rearrangements of the three-dimensional DNA organization result from differential CTCF binding that may comprise regions of up to 100,000 base pairs"

With the CancerEpiSys consosrtium we currently mapping nucleosome positions and epigenetic modifications in primary tumor cells from patients with chronic lymphocytic leukemia to identify patterns of deregulated chromatin organization that can be related to the cancer disease state.

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

Teif, V. B., Beshnova, D. A., Vainshtein, Y., Marth, C., Mallm, J.-P., Höfer, T. & Rippe, K. (2014). Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Res. 24, 1285-1295. doi: 10.1101/gr.164418.113 | Abstract | Reprint (3.3 MB)

Read the English press release or the German press release from the DKFZ.

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