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To connect gene expression to transcriptional control we link mRNA expression to the promoter elements with cap-analysis gene expression (CAGE) technology. CAGE profiles mRNA expression, as well as other capped non-coding RNA (ncRNAs) by high-throughput sequencing with second and third generation sequencers of short tags corresponding to 5‘ ends of mRNAs.
CAGE has allowed comprehensive mapping of human and mouse promoters and to reconstruct transcriptional networks, as well as identifying ncRNAs including antisense. Additionally, CAGE allowed mapping the expression of repeat elements. Analysis of individual cells is of paramount importance to identify the molecular role of RNAs in the cell. We have recently developed nano-CAGE, which is used to profile 1000 or less, and are currently pushing the methods towards single cell. We are also developing robotics and microfluidics to handle single cells. We have collected comprehensive datasets from homogeneously purified neurons. Analysis of mouse olfactory epithelia mapped the promoters for the majority of the mouse olfactory receptor genes.
Other projects involve the comprehensive characterization of the A9 dopaminergic neurons of the midbrain, with identification of specific networks. We are further using nanoCAGE on individual neurons types involved in the brain plasticity and on RNAs deriving from subcellular fractions. |
