Scientist Stories: Piero Carninci, An Atlas of Human Long Non-Coding RNAs

25 Aug 2024 · 39 min
39:17

In this talk, Piero Carninci describes the evolution of his laboratory’s technology platform—from full‑length cDNA cloning to Cap Analysis of Gene Expression (CAGE)—and how it enabled the creation of the FANTOM consortium’s massive transcriptional atlas. He explains how CAGE was applied to thousands of primary human and mouse samples to map >200,000 transcription start sites, generate the largest catalog of promoters and enhancers, and discover tens of thousands of long non‑coding RNAs (lncRNAs) and enhancer RNAs (eRNAs). The presentation highlights functional follow‑up work: (1) linking non‑coding elements to disease‑associated GWAS/eQTL signals (e.g., a Crohn’s disease enhancer); (2) systematic perturbation of antisense lncRNAs, especially the UCHL1 antisense, which unexpectedly increased protein output via a conserved B2 element; (3) genome‑wide chromatin‑RNA interaction mapping that shows both coding and non‑coding RNAs binding distal loci, sometimes across chromosomes. Carninci also outlines the next frontier—single‑cell CAGE profiling of non‑polyadenylated RNAs—to extend the atlas to the Human Cell Atlas, and he points the audience to the publicly available Zenbu browser and data downloads. The talk ends with acknowledgments to the many collaborators and funding bodies, emphasizing that the work is an ongoing community resource rather than a finished product.

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