Can you tell us a bit about yourself and your background?
I come from Menorca, a tiny Spanish island in the Mediterranean Sea. Before starting my studies at the University, I went to the Spanish equivalent to Høgskole to take a degree as a computer technician and another one in commercial scuba diving in Tenerife. After that, I moved to Barcelona to study my Bachelor in Biomedicine at the University of Barcelona, where we focused on the molecular basis of disease and got some wet lab training. I then went on an Erasmus stay to a systems biology group in Trondheim, where I worked as a research assistant while I was taking a Master’s in Bioinformatics and Biostatistics. After finishing, I came to Oslo to work on my PhD at Anthony Mathelier’s lab.
Can you describe your PhD project - what research questions were you trying to answer?
My PhD was focused on the computational study of transcriptional regulation. Transcriptional regulation is a process that allows cells to control which parts of their DNA is actively being transcribed into a product, at a given time. Transcription of DNA is mediated by a group of proteins called transcription factors. Transcription factors can interact with parts of the DNA known as cis-regulatory regions that influence when and where a gene is transcribed. The set of active/inactive transcription factors and regions of DNA they bind to depends on the cell type and its state.
The interplay between cis-regulatory regions and transcription factors is at the core of transcriptional regulation. To better understand how transcription factors interact with the DNA, I was involved in the latest updates of the JASPAR and UniBind. The JASPAR resource provides computational models indicating the preferred DNA sequences for many different transcription factors across several taxonomic groups. The UniBind database contains high confidence predictions of direct transcription factor-DNA interactions, termed transcription factor binding sites (TFBSs).
During the second part of my PhD, I focused on how mutations in cis-regulatory regions can be related to disease. More specifically, we are exploring the accumulation of high impact mutations in cis-regulatory regions in the context of cancer. I am currently working at the Ullevål University Hospital to finish this project.
What were the main findings from your project and what is their significance to this area of research?
With the JASPAR and UniBind databases, we increased the current knowledge of transcription factor sequence preferences and their target DNA regions in a given context. This contextual information is very important in transcriptional regulation. For example, all TFBSs in UniBind are annotated with information such as the cell line/tissue and experimental conditions under which the TFBSs were detected. To make the data in UniBind more accessible, we developed tools that simplify the analysis of user data. For instance, the UniBind's TFBS enrichment tool can be used to study which transcription factors show an enrichment of binding sites in the user’s data.
What did you think was the most interesting part of your work?
Developing databases and tools that can be useful for the research community was something I really appreciated. While not groundbreaking in itself, I think this type of work is very useful for many people in their own research.
How have you found being a PhD student at NCMM?
I really enjoyed it! I got to know a lot of very cool people from all over the world and I felt very supported during the whole period. I learned a lot from the work/life balance I saw in the Norwegian society.
What are your plans for the future?
I plan to continue working in research, but I am very open when it comes to topic and academia or industry. The hope is to find a position in Switzerland to be closer to family (and I’m not going to lie, also closer to the sun).