Extra SciLifeLab The Svedberg seminar, Piero Carninci, Transcriptome complexity
Tuesday September 19
co-hosted with KVA and the Japanese Society for the Promotion of Sciences (JSPS)
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
Piero Carninci obtained his doctoral degree at the University of Trieste, Italy in 1989. From 1990 to 1995 he developed technologies for DNA extraction and DNA sequencing at Talent, a spin-off biotech. He moved to Japan in 1995 at RIKEN, Tsukuba Life Science center and became tenure researcher in 1997. Since 2008 he is a Team and Unit Leader and a Deputy Project Director at the RIKEN Omics Science Center in Yokohama.
An emerging landscape of transcriptome complexity
Gene regulatory elements are key to understand health and diseases. Mapping 5’-ends of RNAs is the key to understand the gene regulation as they identify promoters. 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). The project also explored complexity of genome activation hierarchy in which transcription initiates with enhancer followed by promoter and then other genes (Arner et al. Science 347, 1010, 2015). 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 (Hon et al. Nature 543, 199, 2017). Ongoing FANTOM6 aims to create the broadest database of functional lncRNAs, as a valuable resource in the community.
Host: Ulf Landegren (firstname.lastname@example.org)
Venue: Trippelrummet, ground floor SciLifeLab, Husargatan 3.