Open Research Europe presents an interview with Dr Baoxu Pang, Assistant Professor in the Department of Cell and Chemical Biology at Leiden University Medical Centre, and Dr Corentin Claeys Bouuaert, Group Leader in the Louvain Institute of Biomolecular Science and Technology. They are both Guest Advisors of the Genomes Collection on Open Research Europe.
This Collection aims to provide a space to publish the latest European Commission-funded research in understanding genomes dynamics, organization and stability, and their role in gene regulation.
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 Genomes?
Dr Baoxu Pang: My group focuses on the study of the non-coding regulatory genome, especially the characterization of silencer elements and their roles in biology. The non-coding regulatory elements control gene transcription, which is one of the key topics covered by the Genomes Collection. The non-coding regulatory genome contains the “switch buttons” to control the on/off and the intensity of the expression of genes in cells. With the help of the non-coding regulatory genome, it is possible the complex human body could be formed based on a single genome blueprint.
Dr Corentin Claeys Bouuaert: My laboratory is interested in the mechanisms of DNA recombination involved during meiosis. To put it simply, we study how organisms transmit their genetic material to their offspring. In the case of humans, we have 46 chromosomes, half of them inherited from our mother and the other half from our father. In order to generate reproductive cells, these 46 chromosomes have to be separated in two. This happens through meiosis, a complex mechanism that allows the 23 pairs of chromosomes first to find each other before they can be separated. In order to do that, the cells start by breaking their DNA on purpose. The breaks will then be repaired by a mechanism called homologous recombination. It is this recombination process that allows the chromosome pairs to recognize each other. In addition, during this process, the chromosomes exchange fragments. This genetic shuffling is the reason we are all different.
Our field of research touches upon different aspects of genome biology, including the mechanisms of DNA repair, the role of chromosome organization, and the impact of transcriptional and post-transcriptional regulatory networks.
What are the biggest challenges of being a researcher in your field?
Dr Baoxu Pang: One of the biggest challenges is to understand how the genome operates, specifically to identify and assign functions to the non-coding genome in different tissues. As there are more than a few hundred different cell types or tissues in our body, and the non-coding genome functions in a tissue-specific manner, the same piece of non-coding genome fragment may function differently in different tissues.
Dr Corentin Claeys Bouuaert: My field of research has a long history, with many decades of research that have brought a wealth of insights into the intricate molecular mechanisms involved during meiosis. Yet there remain many important questions to address. As a researcher, I think one of the challenges is to develop innovative approaches to be able to ask questions that could not be addressed before.
What are the major questions your research area tries to answer?
Dr Baoxu Pang: To me, one of the major questions the field tries to answer is to determine the general signatures of distinct functional genomic units. Once we could extract some general signatures of the different non-coding genomic units, it is possible to predict the function of these elements in different tissues.
Dr Corentin Claeys Bouuaert: In our field, one of the key challenges is to understand the intimate relationship between events that happen at different scales. The molecular events of DNA recombination during meiosis are coupled to chromosomal-scale genome organization. This is something that is very difficult to investigate because most experimental approaches are suited to ask questions at a specific scale.
Why is open science important to you and researchers in your field?
Dr Baoxu Pang: One of the most helpful elements for my field that open science promotes, and the Open Research Europe supports, is the publication of “negative” results. Such results are often not accepted in other, traditional forums, but can help researchers to avoid wasting time and resources on the same topics. Instead, researchers can focus on answering new questions, which can help to accelerate the speed of discoveries.
Dr Corentin Claeys Bouuaert: Generally speaking, I think our field has been very favorable to open science movements. Posting preprints has become routine. Researchers present unpublished work at conferences. Data and codes are made available. I think everyone wants to help push the field forward and understands that withholding information until after publication slows down research unnecessarily.
In addition, lots of high-quality research is published in open-access journals, although there are still important barriers to overcome. In particular, the perceived necessity to publish in ‘high impact’ journals.
Are there any challenges to participating in open science within your research area?
Dr Baoxu Pang: The key challenges are to keep the results solid; and to make the results reach a broader audience. As some open science outputs are published first without peer review, for many audiences it is hard to judge the quality of the research.
Dr Corentin Claeys Bouuaert: I don’t think there are any challenges specific to my research field; I think of it more as a systemic problem, in part due to the competitive nature of the system. One challenge is that some researchers perceive this ‘openness’ as helping their competitors. Hence you sometimes see important methodological details missing from publications so that researchers can keep an edge over the competition, or codes, data, and reagents are not shared for similar reasons. I don’t see this much in my field, and I think the mentalities are changing, but some researchers certainly think like that.
Another challenge specific to open access publishing is that in some journals, the costs to publish open access are often prohibitively high. Luckily, there are preprint servers that partially solve that problem. But only partially, because even though the research is made publicly available, it may not have the visibility of the journal-published article.
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Learn more about the scope and content included in the Genomes Collection .
