Vipin Kumar, postdoctoral researcher in the Mathelier group at NCMM, visited the group of Pelin Sahlén at SciLifeLab, to finalize their analysis for the FANTOM6 project. FANTOM6 is a worldwide collaborative project, aiming to systematically elucidate the function of long non-coding RNAs (lncRNAs) in the human genome.
This ambitious goal requires a wide range of expertise, and with the support from EATRIS-Plus Staff Exchange Program, Kumar was able to visit the Sahlén group in Stockholm, Sweden, for a week in October to combine their knowledge.
Combining expertise to develop data analysis pipeline
Kumar’s work has focused on determining the location of lncRNA around DNA, to help elucidate their potential role in regulating gene expression.
– LncRNA comes in many types, shapes, and sizes. To understand how they may influence gene expression, we are working on finding areas of the DNA that attracts lncRNA. If we find that certain lncRNA’s cluster to a specific area of the DNA, it could give us an idea of the lncRNA’s function there, says Kumar.
To do this, he has been developing a bioinformatic pipeline to analyze large amounts of sequencing data. Having met at a consortium meeting last year, Kumar and Sahlén realized that by combining their data, they would be able to develop a more detailed and accurate analysis pipeline together.
The Sahlén group had gathered data that included the structure of the DNA that could indicate if some areas of the DNA are more accessible than others.
Collaboration was important for reaching project goal
A chat with Anita Kavlie, national coordinator for EATRIS Norway, encouraged Kumar to apply to the EATRIS-Plus Staff Exchange Programme to visit the Sahlén group.
The outcome of the visit was the development of a more detailed and accurate data analysis pipeline to answer the questions: where does the lncRNA come from, where is it going, and what is it doing there?
– Adding information on DNA structure improved our analysis. The main output was an updated data analysis workflow or pipeline that better accounted for technical bias. We were also able to define more clearly the relationship between RNA-interactions and DNA-structure. This clarification helped lay the foundation for analytical integration of these two aspects of genome biology, says Kumar.
EATRIS supports staff exchange and activities
– Being able to visit and meet in person with support from the EATRIS-Plus Staff Exchange Program was definitely useful for efficiently developing the pipeline. Our discussions were also helpful for defining the specific questions we wanted to answer, and how to interpret the results of our analysis, concludes Kumar.
In addition to the EATRIS-Plus Staff Exchange Programme, researchers in Norway were supported by the EATRIS NORWAY node reward received in 2022.
The money from the Node reward supported the following activities:
- Camila Esguerra’s visit to Dr Rima Nabbout, a pediatric neurologist and a top international expert on epilepsy syndromes. The purpose of the visit was to forge a collaboration with Rima and her team, and the meeting has already led to some exciting new developments
- Sponsored five scientists from Oslo University Hospital and the University of Bergen to attend the first Nordic ATMP meeting in Uppsala, Sweden.
- Cover course fees to attend TMeX (Translational Medicine explained) in Berlin, Germany, in collaboration with Bayer for two persons from UiO Growth House.
- Sponsor a scientist from University of Bergen to attend the second Nordic ATMP Meeting to present the Norwegian ATMP landscape, and to attend the following annual ATMP Sweden meeting in Uppsala, Sweden.