Lights on… Marc Marti-Renom, creator of TADbit

Marc Martí-Renom is a professor at the Catalan Institution for Research and Advanced Studies (ICREA) in Barcelona (Spain). After a Ph.D. in Biophysics from the Autonomous University of Barcelona (UAB) where he worked on protein folding under the supervision of Professors B. Oliva, F.X. Avilés and M. Karplus (Nobel Laureate in 2013), Marc joined the Sali Lab (Rockefeller University, New York – USA) for a postdoctoral fellowship on protein structure modelling. Later on, he was appointed Assistant Adjunct Professor at the University of California, San Francisco (UCSF). Back in Spain, Marc was the head of the Structural Genomics Group in Valencia at the Principe Felipe Research Center (CIPF). Since October 2013, he is full time research Professor at ICREA and leads the Genome Biology Group at the National Center for Genomic Analysis (CNAG) and the Structural Genomics Group at the Centre for Genomic Regulation (CRG), both in Barcelona.

His group is broadly interested in the molecular mechanisms that regulate cell fate, from the structure prediction of macromolecules to the determination of nuclear organisation. In the past few years, they developed TADbit, a python library that extend the modelling capacities of IMP to study the structure of genome or genomic domains based on high-throughput chromatin conformation capture (3C) data. Together with TADkit, a 3D genome browser that allows visualisation and annotation of 3D models, TABbit provides a stable and friendly framework to build 3D genome structures, explore their dynamics and facilitate their analysis.

1) Can you introduce your software in a few words?

We develop software that aim at modelling, analysing and visualising 3D genomics datasets, including 3C-based data, Chip-Seq data and expression data. The goal of our software (called TADbit and TADkit) is to help researchers world-wide in their needs for characterising the genome structure in three dimensions.

2) Regarding the development model of your software, who is in charge of the development/maintenance/support?

We have two researchers (one more biology oriented and another one more computation oriented) that take care of the development and maintenance of our software. However, every single member of the group contributes with several modules of the software.

3) In which regards does your software fall within the field of integrative modelling?

We have developed TADbit to be able to deal with diverse sets of experimental data that explain how the genome folds in space and time. In this regards, it can be called an “integrative” approach. Unfortunately, we do not always have the chance of using diverse sets of orthogonal data, which would be the optimal application of TADbit.

4) Can you share with us an example in which the use of your software was key to answer a scientific question?

Sure, we have already published four articles where TADbit and 3D models from TADbit were key elements of understanding a biological question. Those include:

Trussart, M., Yus, E., Martinez, S., Baù, D., Tahara, Y.O., Pengo, T., Kretschmer, S., Swoger, J., Miyata, M., Marti-Renom, M.A., Lluch-Senar, M. and Serrano, L.
Defined chromosome structure in a genome-reduced bacterium, Mycoplasma pneumoniae.” Nature Communications (2017) 8 14665

Le Dily, F., Baù, D., Pohl, A., Vicent, G.P., Serra, F., Soronellas, D., Castellano, G., Wright, R.H.G, Ballare, C., Filion, G., Marti-Renom, M.A. and Beato, M.
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation“, Genes & Dev. (2014) 28 2151-2162

Umbarger, M.A., Toro, E., Wright, M.A., Porreca, G.J., Baù, D., Hong, S-H., Fero, M.J., Zhu, J., Marti-Renom, M.A., McAdams, J.H., Shapiro, L., Dekker, J. and Church, G.M.
The three-dimensional architecture of a bacterial genome and Its alteration by genetic perturbation“, Molecular Cell (2011) 44 252–264

Baù, D., Sanyal, A., Lajoie, B.R., Capriotti, E., Byron, M., Lawrence J.B., Dekker, J. and Marti-Renom, M.A.
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules“, Nature Structural and Molecular Biology (2011) 18 107-114

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