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Piero Carninci, Ph.D. - "An emerging landscape of transcriptome complexity"

Deputy Director, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
When Jun 15, 2018
from 11:00 AM to 12:30 PM
Where Tigem, Auditorium "Vesuvius"
Contact Name
Contact Phone 08119230659
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Short CV

Abstract
Mapping 5’-ends of RNAs is the key to understand the gene regulation as they identify promoters, as well as long non-coding RNAs (lncRNAs) with functions. In order to comprehensively understand regulatory elements, we developed the Cap Analysis of Gene Expression (CAGE) technology, which enables to identify transcription start sites (TSSs) and quantitatively measure their activity throughout the genome at high-throughput. In the RIKEN Functional Annotation of the Mammalian Genome 5 (FANTOM5) project, we created a very broad map of the promoterome and regulatory networks by simultaneously mapped mRNAs and lncRNAs TSSs and measured their expression at each different promoters with CAGE, on a comprehensive panel of human and mouse primary cells and other tissues. The study revealed the existence of 223,428 and 162,264 promoters and 65,423 and 44,459 enhancers, in human and mouse respectively, which are often tissue specific (Forrest et al. Nature 507, 462, 2014, Andersson et al. Nature 507, 455, 2014). Using CAGE, we also built an atlas of human lncRNAs with accurate 5’-ends (Hon et al. Nature 543, 199, 2017). Classification of lncRNAs revealed that most intergenic lncRNAs are derived from enhancer-like regions rather than classic promoters and GWAS trait-associated SNPs enriched at lncRNA loci were specifically expressed in cell-types relevant to the specific diseases, suggesting their roles in diseases.
Ongoing FANTOM6 project is aiming at creating the broadest database of functional lncRNAs, as a valuable resource in the community. Most lncRNAs are localized in the cell nuclei. In order to explore their regulatory functions, we recently developed a new technology named RNA and DNA Interacting Complexes Ligated and sequenced (RADICL-seq) that precisely maps genome-wide RNA-chromatin interactions in intact nuclei with the directional information of the RNA tags.
Furthermore, we are pursuing a strategic collaboration with the International Human Cell Atlas (HCA) project, which is aiming at the creation of a comprehensive map of all human cell types and states at single cell level, with our newly developed single cell CAGE.

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