The Friedländer group applies beyond-state-of-the-art computational and Omics methods to address fundamental questions in RNA biology. Our focus is on quantitatively describing and functionally characterizing mammalian transcriptomes, and methods include next-generation sequencing of single and pooled cells, as well as development of new algorithms and and experimental methods.
Of particular interest to us are microRNAs: 22 nucleotide long RNA molecules that regulate protein-coding genes in all multi-cellular animals. Since they confer regulation on the majority of human genes, it is not surprising that microRNAs are involved in numerous biological processes – including diseases such as metabolic and neurodegenerative diseases and cancer. Even though microRNAs have been systematically studied for more than twenty years, fundamental questions regarding their evolution, biogenesis and function remain unanswered.
We study microRNA function by profiling these regulators and their gene targets in the single cells where the interactions between them occur. From the measurements we infer copy-per-cell numbers for the transcripts, and we develop mathematical models to describe the kinetics of regulation. For this purpose we apply single-cell sequencing and screening methods. Recently, we have developed a method to detect microRNA targeting in single cells, using an editing-capable TRIBE fusion protein (unpublished). To address evolutionary aspects of microRNAs, we compare microRNAs between representatives of all major animal groups, using the highly curated MirGeneDB database – that we have contributed to developing.
Our recent research include studies of microRNA biogenesis in living cells, discovering authentic RNA molecules in ancient samples from the Siberian permafrost, and profiling microRNAs in astronaut blood in collaboration with NASA (see our Publications).
Our group is part of Stockholm University but is located at the SciLifeLab hub. We work closely with the research groups of Claudia Kutter and Vicent Pelechano (both at the Karolinska Institute) – for instance having joint lab meetings and journal clubs. Our research is funded by the Swedish Research Council (VR), the Swedish Strategic Research Areas (SFO), the Swedish Cancer Foundation (Cancerfonden) and a starting grant from the European Research Council (ERC).
The Friedländer group is balanced between researchers with wet-lab and dry-lab expertise. We focus on wet-lab methods that concern RNA biology and mammalian cell culture experiments. We extensively generate standard and custom next-generation sequencing libraries that we sequence on our Illumina NextSeq instrument, which is shared with five other research groups.
Our dry-lab expertise is focused on sequence analysis, with special focus on next-generation sequencing transcriptome analyses. We apply standard software and also develop our own solutions for highly custom data. MicroRNA discovery is one of the key strengths of the Friedländer lab: members of our group have developed miRDeep(2) which is currently the most widely used method for microRNA discovery.