Open Research Europe presents an interview with Dr Germano Cecere, director of the Mechanisms of Epigenetic Inheritance Unit at Institut Pasteur in France, and Dr Jop Kind, Developmental Epigenomics group leader at Hubrecht Institute in The Netherlands. They are both Guest Advisors of the Epigenetics Collection on Open Research Europe.
Epigenetics is an emerging area of research that studies how the environment and one’s behaviors can affect gene expression. Unlike genetic changes, epigenetic modifications are reversible and do not change DNA sequences, but how DNA sequences are read by our cells.
In this Collection, we publish research on general epigenetic processes such as DNA methylation, histone modification, gene regulation and gene expression, DNA damage and repair, and epigenetic inheritance.
Read on to find out more about the work of our Guest Advisors, their challenges, and why they think that open science is important for their fields.
What is your research area and how does it relate to Epigenetics?
Dr Germano Cecere: My area of research is epigenetic inheritance. We are investigating the possibility that in addition to DNA, we inherit other molecules that can help memorize and transmit our ancestors’ life experiences. Our research focuses on small pieces of RNA called small RNAs, which can act as carriers of information about an individual’s experiences and environmental exposures. These small RNAs can be passed down to future generations, potentially influencing the expression of their genes and leading to the inheritance of traits and characteristics beyond just DNA sequence. We are currently exploring the mechanisms by which small RNAs transmit this information, which will help our understanding of inheritance and disease heritability.
Dr Jop Kind: My research group is interested in understanding how chromatin and spatial genome organization contribute to gene regulation in early embryogenesis. Every cell contains 2 meters of DNA that needs to be condensed into the tiny space of a cell’s nucleus. This organization is unique to every cell, and, for new traits to arise, different regions of the DNA need to become accessible and active. The open and closed configurations of DNA are associated with different epigenetic modifications that help guide the correct coordination of gene regulation and the positioning of DNA in the 3D space of the nucleus.
We have pioneered the development of methods to map and visualize 3D genome organization, chromatin and epigenetics in single cells. From these studies we hope to acquire detailed information on the mechanisms by which epigenetics helps control gene regulation and, in general, the process of cell-fate choice. Better knowledge of this process will also help us understand why gene regulation sometimes goes wrong during developmental failure or the establishment of pathologies like cancer.
What are the biggest challenges of being a researcher in your field, or more widely?
Dr Germano Cecere: There are several challenges for being a researcher addressing fundamental questions in biology.
First, the availability of funding schemes that support projects based on curiosity-driven questions. Currently, the European Research Council funding scheme is the only fund to support this type of research, and I hope we have more of these kinds of funds in Europe to support research in the future.
The next challenge is related to attracting talented young researchers, such as Ph.D. students and postdocs, willing to conduct such pioneering research. This has become more difficult in recent years and is incredibly challenging for the not-as-well-established teams in countries where the salaries of Ph.D. students and postdocs are less competitive.
A final challenge is related to the conceptual framework defining our research projects. The need to finalize results and publications relatively quickly, especially for 2-3-year funding schemes, does not favor more explorative research that may take longer, but still lead to a groundbreaking discovery. In this regard, fostering collaborative research, interdisciplinary approaches, and developing new methodologies are essential aspects that can help overcome such difficulties.
Dr Jop Kind: In general, the biggest challenge as a researcher is to establish your niche and refine that niche during the different phases of a career.
The initial phase, establishing a research group, can be stressful but often involves continuing postdoctoral work, and the funding options are competitive but plenty.
The second phase occurs when the group is established, has transitioned into new research areas, and finished the first round of funding. In this stage, the group needs to reconsider the direction and define what the program will be in the next ten years.
I think this is extremely challenging. It feels natural to simply continue the same path, but you need to consider whether you are still in the best position to pursue this trajectory, or whether others are more capable of doing so. And perhaps there are other technologies/methodologies that are more suited to address the research questions you have. You want to keep challenging yourself and the group and continue evolving.
However, in terms of funding, this is rather tricky. The funding opportunities are generally more competitive, and it is difficult to obtain grants for new projects without a proven track record.
Why is open science important to you and researchers in your field?
Dr Germano Cecere: Open science is the foundation to build trust and improve reproducibility in our field of research. Besides depositing genomic data in publicly available repositories (an essential part of our research program), we should also improve the details of analyses and methods described in our work. Often, methods still need to be fully explained for complex or novel research but, due to space limitations in traditional scientific journals, this is not always achievable. This can cause a lack of reproducibility and trust in published data.
Moreover, the publication of “negative” results is also an essential aspect of our research to help evaluate experiments that do not give the expected outcome.
An open research platform like Open Research Europe can help address these challenges.
Not only does it publish multiple article types to support all outputs of a research project, including dedicated Method Articles and Data Notes, it also supports publication of null, confirmatory, or negative results, where experiments can be openly discussed. This can benefit all scientific readers, not just experts in the specific field of study.
Similarly, access to the whole publication process, including editorial correspondence and the reviewing process, should be fully open in any scientific journals and publications, as is the case for Open Research Europe. It is essential to read the critical opinion of scientific experts for a specific study, highlighting the study’s importance and limitations.
Finally, fostering collaborative work instead of having multiple labs independently working on similar questions will improve the efficiency of addressing critical scientific questions in the field and enhance data reproducibility. This can also allow the deposition of in-progress datasets without the risk of being scooped by another team of researchers.
Dr Jop Kind: Open science is extremely important and in particular, data sharing/accessibility of publicly available repositories is essential for our research area.
We very frequently make use of other people’s data to cross-reference our own work or to place our samples in a broader context. Especially today, with massive collections of data like the human cell atlas, it is extremely valuable to facilitate open and easy access to such data.
Are there any challenges to participating in open science within your research area?
Dr Germano Cecere: The cost of open-access publications is still very high, which is undoubtedly one of the main barriers to choosing an open science publication. Currently, only labs with sufficient funds can afford open access publications. Strategies that help overcome this significant barrier will allow more researchers to opt for open-access publications. In addition, increasing the number of open-access articles being published can help convince more people of the benefit that derive from them.
Dr Jop Kind: A major concern regarding open access publications is the costs. Without subsidies by employers, many are not able to afford it. This obviously creates a barrier to publishing open access in journals that are not “open” by default. Good progress has been made towards open access science, but obviously, there is still a long way to go to make all science accessible to everybody. I therefore highly support initiatives like Open Research Europe to make this possible.
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