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Call for standards of epigenetic data

At the heart of every cell is the nucleus, which acts as the cell’s control center. Recent studies have revealed more and more information about its organization and dynamics. However, the rapid development of methods and the increasing complexity of the collected data pose major challenges. In ‘Nature Genetics’, leading scientists in the field have therefore called for uniform standards of epigenetic data. Among them is Maria Elena Torres-Padilla of Helmholtz Zentrum München.

© Spencer Phillips/EMBL-EBI

The nucleus contains all the information needed for survival of the cell and the organism in the form of the genetic information - the DNA. The DNA is intricately packaged in order to fit all the information into the cell nucleus and to make the genes accessible at the right time. “We are currently endeavoring to understand the organizational levels and to find out how they change over time, for example in the course of development or during the emergence of diseases,” explains Prof. Dr. Maria Elena Torres-Padilla, Director of the Institute of Epigenetics and Stem Cells (IES) at Helmholtz Zentrum München. She is an expert in epigenetics, which studies, amongst other things, how our genes respond to the environment.

She and her international colleagues are making good progress, for example in the context of the 4D Nucleome network. “The aim is to create a kind of atlas for all the different types of cells that captures the three-dimensional organization of the nucleus and documents how it changes over time, thus 4D for the fourth dimension,” Torres-Padilla explains. In this way, she and her colleagues hope to discover fundamental mechanisms underlying the fate of cells and in the long term to find out how a single cell develops into a fully-fledged organism.

Opportunities and challenges of new technologies

However, new technologies and mushrooming data volumes are creating new challenges along this path. “As exciting and promising as current developments are, we now see a good opportunity to unite our efforts. We, as 4D Nucleome members, are therefore proposing measures to establish uniform standards. This applies both to the technologies used and to the documentation of the results and how they are shared with the international research community.” In this way, the scientists want to ensure that information is integrated and resources are used efficiently.

The 4D Nucleome Network is a main pillar of the LifeTime Initiative, which was set up in 2018 and is also supported by the Helmholtz Association. As part of this project, experts from science and industry aim to reliably predict, when a disease is likely to become manifest and what course it is likely to take. The founding members include IES Director Professor Maria Elena Torres-Padilla and Professor Fabian Theis, Director of the Institute of Computational Biology at Helmholtz Zentrum München.

“Through the LifeTime initiative and collaborations with industrial partners, our results will have even great impact,” says Torres-Padilla. “Our overall aim to provide the information through which physicians may give earlier diagnosis and treatment regimens according to the molecular state of a patient’s tissues is incredibly important, and exciting.  This is a 10 year game-changing vision, which will be enabled through the participation of many stakeholders and includes large aspects of both basic and applied research across Europe, as well as key strategic collaborations with our industrial partners.”

Further Information 

A press release on the large-scale LifeTime project written by Helmholtz colleagues of the Max Delbrück Center for Molecular Medicine (MDC) in Berlin can be found under the title “LifeTime – a visionary proposal for an EU Flagship”.

Original Publication:
MA. Marti-Renom et al. (2018): Challenges and guidelines toward 4D nucleome data and model standards. Nature Genetics, DOI: 10.1038/s41588-018-0236-3

As German Research Center for Environmental Health, Helmholtz Zentrum München pursues the goal of developing personalized medical approaches for the prevention and therapy of major common diseases such as diabetes mellitus, allergies and lung diseases. To achieve this, it investigates the interaction of genetics, environmental factors and lifestyle. The Helmholtz Zentrum München has about 2,500 staff members and is headquartered in Neuherberg in the north of Munich. Helmholtz Zentrum München is a member of the Helmholtz Association, a community of 19 scientific-technical and medical-biological research centers with a total of about 37,000 staff members. 

The research of the Institute of Epigenetics and Stem Cells (IES) is focused on the characterization of early events in mammalian embryos. The scientists are especially interested in the totipotency of cells which is lost during development. Moreover, they want to elucidate who this loss is caused by changes in the nucleus. Their main goal is to understand the underlying molecular mechanisms which might lead to the development of new therapeutic approaches.