“Understanding the cell repertoire through gene regulation”

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Gene regulation is a key concept in molecular biology. Untangling interaction between genes and the molecular mechanisms involved in such interactions provides insights in many topics, for example, the cell specialization. Anamaria studies how transcription factors, a set of proteins, bind to certain genes and how that affects their regulation and posterior cell differentiation at Sebé-Pedrós laboratory.

What did you study and why did you choose it?

I did both my Bachelor and Master thesis in Molecular Biology, during which I got an extensive theoretical and a decent experimental education, but I found that most of the courses I have been taking were lacking a quantitative approach. That’s why during my Master’s degree I chose to specialize in Computational Biology. This ultimately led to doing my Master’s thesis project in Bioinformatics, after which I worked for eight months as a Bioinformatician in the sequencing facility, further learning the ropes of my future trade, before eventually starting my PhD.

Did you plan to do research when you finished your degree? What motivated you to dive into research? What lines of research does your laboratory follow?

My Master’s degree was largely focused on tools development, and even though I found it interesting and worthwhile, I also wanted to do research after graduating. However, back then I only knew I wanted to work in bioinformatics – more precisely, genomics – but I did not have a specific question which I wanted to commit myself to, so I took some time to decide what to pursue. And I think it was a good choice, as it both gave me time and space to decide on what I want, as well as to get more experience in practical aspects of bioinformatics. Ultimately, I narrowed my interest down to evolution (if you can call that narrowing down – after all, nothing in biology makes sense except in the light of evolution!), the underlying mechanism behind all biological mechanisms, from micro to macro scale, from organism development to cancer development – evolution is the thread running through it all. This was something I decided I want to focus on, so I joined the lab, which studies gene regulation from the evolutionary perspective, using the latest single-cell sequencing methods. In this way, both my requirements in terms of research methods and topic were met.

Could you explain what your research is about?

I am trying to characterize gene regulatory logic that drives cell type specific gene expression. I am working with gene expression and chromatin data from non-bilaterian animal species – these include sponges, ctenophores, placozoans and cnidarians, and at the moment, I am mostly focusing on the latter. These species all have a relatively small number of well defined major cell types (neurons, secretory cells, epithelia, etc.), and are amenable to whole-organism single-cell sampling, which means that we can completely and impartially characterize their cell types repertoire, without limitations imposed by the need for isolating individual tissues and organs. Moreover, because of their phylogenetic position at the root of animal tree of life, they are maximally informative for reconstructing the evolution of major animal cell types and their associated gene regulatory mechanisms. To characterise these mechanisms, I am integrating gene expression and open chromatin data to identify transcription factor (TF) binding motifs in the regulatory regions of genes with cell-type specific expression. The goal of my project is to understand how various TFs interact with their target genes and between each other, leading to the establishment and the maintenance of cell type specific expression programmes, and how these mechanisms differ and evolve between different species.

What do you plan to do when you finish your PhD?

In the middle of my second year of PhD, I still don’t have a clear picture of what I would do afterwards, but I know I want to continue working in bioinformatics – maybe on a different research question, or focusing on novel methods.

What activities do you do in your spare time?

I enjoy traveling and spending time in nature, hiking and jogging, and for me this is the best way to step back from everyday work routine and get a breather. I also like to take part in teaching and organising courses – including an awesome summer school in bioinformatics, NGSchool – because for me this is usually not a one way process and I learn a lot from these events myself.

What would you say to someone who is finishing a degree in Bioinformatics?

To an undergrad finishing a degree in Bioinformatics I would say ‘Well done’, because you have made a good choice and you have many options to choose from if you are happy to continue working in this field – even if you are not pursuing a PhD, there are alternative, less traveled but definitely worthwhile career paths. And to fellow graduate students finishing a degree in bioinformatics, I would say ‘Well done’, too, and ask them about their plans for future, because I expect there could be many interesting answers.

Alexis Molina, BDBI Alumni
Laura Serra, BDBI Student