Laboratory for Applied Computational Genomics

Current Research

 

As shown by the FANTOM, ENCODE, and other projects, mammalian genomes produce a huge number of different transcripts. Most of these transcripts do not code for protein, but are non-coding transcripts that are thought to function as regulatory RNAs. Long non-coding RNAs (lncRNAs) in particular have been shown to act as key regulators in a wide range of biological roles, and have been implicated in human disease in genome-wide association studies.

While the function of proteins can be predicted based on the amino acid sequence inferred from the mRNAs’ nucleotide sequence, the primary sequence of non-coding RNAs is poorly conserved between homologs, and in most cases cannot be used to predict their function.

The goal of FANTOM6 is to elucidate the function of non-coding RNAs on a large scale. To this purpose, we combine knockdown experiments in multiple cell types, followed by molecular phenotyping using CAGE transcriptome profiling to assess the response of the cell to the perturbation and to identify the molecular pathways in which the non-coding RNA may function. In addition to the knockdown response, we are currently investigating approaches based on 3D genome maps to infer the function of non-coding RNAs.