Toronto, ON, CAN. Scientists have described the 3D structure of a key protein component involved in enabling the copying of "epigenetic code" from cell to cell. The code is a series of chemical switches that is added onto our DNA in order to ensure our cells form various tissue types (e.g., liver and skin, despite identical DNA genetic code.

 

Proteins perform many of the essential functions in the human body. When a protein, or a group of proteins, fail to act in their normal way, we are prone to sickness. Most medicines exploit this by binding to proteins and influencing their activity. Researchers can design drugs with molecules that fit if they know the shape of a protein "target".

 

So, when DNA is copied from cell to cell, it is essential that the epigenetic code is also copied accurately. If not, a liver cell may divide into another type of cell, such as a nerve or eye cell. A breakdown in this system might also mean that a gene for cell growth is accidentally switched on, for example, leading to unregulated cell growth and the development of tumors.

 

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Researchers have determined the 3D structure of a key protein component involved in enabling "epigenetic code" to be copied accurately from cell to cell. Image courtesy of the Wellcome Trust.

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The field of structural genomics is focused on the three-dimensional structures of proteins. Ordinarily. it is very expensive to determine a new protein structure (as much as US$1 million.

 

However, more systematic approaches have become possble with the arrival of methodological improvements, computers, and access to the complete sequence of our DNA (the human genome). The information on structure provides a powerful means to develop a diagram of a protein suitable for further research and implementation in new treatment methds.

 

Research published in 2007 showed the importance of the nuclear protein UHRF1 in ensuring that the epigenetic code is accurately copied. Epigenetic switches are created by the addition of a chemical group (methyl) to DNA in a process known as methylation, facilitated by the enzyme DNMT1. The researchers believe that when this code is copied, UHRF1 ensures the accuracy of the process, like a proof-reader checks a typeset article before printing.

 

The key element of UHRF1 involved in this "proofreading" process is known as the Set and Ring Associated (SRA) domain, but the exact mechanisms by which the SRA domain accomplishes this task were unclear. The journal Nature concurrently published three different articles that facilitate understanding of the UHRF1 structure.

 

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Professor Sirano Dhe-Paganon from the Structural Genomics Consortium (SGC) laboratories at the University of Toronto (Canada). [N1] 

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"Given the increasing focus on epigenetics as a mechanism behind cancer, elucidating the structure of UHRF1 may provide crucial insights into what goes wrong," says Dhe-Paganon.

 

The structural papers not only represent an advance for the epigenetics field, but also an advance for how the science was done. The concurrent publication of the three papers highlights the competitive nature of this field, but in fact these papers were made possible because the SGC, in keeping with its policy of making its data freely and immediately available, made the underlying information available in the Protein Data Bank (PDB) late in 2007. The availability of this information allowed the other groups to make more rapid progress in their own work.

 

"By releasing the structural information into the public databases as soon as it was available, we have ensured that other research groups could make immediate and maximum benefit from the shared knowledge," says Professor Dhe-Paganon.

 

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Professor Masahiro Shirakawa. from Kyoto University (Japan).

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Shirakawa openly acknowledges that the SGC data was crucial to his team's paper, which also appears in the journal Nature. "Structural biology is a complex, but very important field, with the potential to drive forward important research in many areas. The information provided by the SGC significantly speeded up our own work."

 

The SGC's "open source" policy contrasts with the accepted practice in the structural biology field, which is to make the underlying data available only after the work appears in print. However, Professor Al Edwards, Director of the SGC, believes strongly that data such as the 3D structure of proteins should be made freely available as soon as they are discovered.

 

"From the outset, it's been important to us to release our structural data immediately," says Professor Edwards. "This is contrary to the way many scientists work, but we believe it is crucial for facilitating scientific and medical progress, and our policy has not inhibited our ability to publish our work in the top journals. All the protein structures studied by the SGC have medical relevance and making them freely available ensures that scientists are able to use them to make progress in our understanding of disease and the development of new drugs."

 

[N1] The Structural Genomics Consortium (SGC) is a not-for-profit organization that aims to determine the three dimensional structures of proteins of medical relevance, and place them in the Protein Data Bank without restriction. The SGC operates out of the Universities of Oxford and Toronto and Karolinska Institutet, Stockholm. In the period from July 2004 to June 2007, the SGC deposited the structures of 450 proteins from its Target List of ~2,000 proteins, to achieve a deposition rate of 200 structures per year and to reduce the cost/structure to below USD5,000. Research at the SGC focuses on proteins involved in most human diseases as well as diseases, like malaria, caused by parasites. (Desripton courtesy of the Structural Genomics Consortium (SGC)

 

 

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