Piero Carninci

Dr Piero Carninci is a world-leading geneticist, currently Head of the Genomics Research Centre – Functional Genomics Programme at Fondazione Human Technopole in Milan (IT) and Team Leader for Laboratory for Transcriptome Technology at the RIKEN Centre for Integrative Medical Sciences in Yokohama (JP). Piero is responsible for the creation and development of various new technologies for DNA and RNA sequencing and analysis. He has led many large-scale international initiatives, including FANTOM, ENCODE and the Human Cell Atlas. He has published more than 400 papers and he is inventor of 63 patents, including a family of patents on antisense RNA than enhance protein translation (SINEUP RNAs). He is one of the co-founders of TranSINE Therapeutics, now known as Harness Therapeutics, a UK biotechnology company developing a novel class of therapeutic RNAs based on its pioneering SINEUP platform technology.

Relevant Publications

Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P*, Salzberg SL*. The status of the human gene catalogue. Nature. 2023 Oct;622(7981):41-47. doi: 10.1038/s41586-023-06490-x. Epub 2023 Oct 4. PMID: 37794265.”,
FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, et al. (Carninci P 260th of 261 authors) A promoter-level mammalian expression atlas. Nature. 2014;507(7493):462-470. doi:10.1038/nature13182. PMID: 24670764; PMCID: PMC4529748.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787. PMID: 24670763; PMCID: PMC5215096.
Pascarella G, Hon CC, Hashimoto K, Busch A, Luginbühl J, Parr C, Hin Yip W, Abe K, Kratz A, Bonetti A, Agostini F, Severin J, Murayama S, Suzuki Y, Gustincich S, Frith M, Carninci P. Recombination of repeat elements generates somatic complexity in human genomes. Cell. 2022 Aug 4;185(16):3025-3040.e6. doi: 10.1016/j.cell.2022.06.032. Epub 2022 Jul 25. PMID: 35882231.
Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res. 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119. Epub 2020 Jul 27. PMID: 32718982; PMCID: PMC7397864.
Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima Y, Yabukami H, Terooatea T, Sasaki T, Suzuki T, Valentine M, Pascarella G, Okazaki Y, Suzuki H, Shin JW, Minoda A, Taniuchi I, Okano H, Arai Y, Hirose N, Carninci P. Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians. Proc Natl Acad Sci USA. 2019 Nov 26;116(48):24242-24251. doi: 10.1073/pnas.1907883116. Epub 2019 Nov 12. PMID: 31719197; PMCID: PMC6883788.
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y. Transcribed enhancers lead waves of coordinated transcription in transitioning. Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12. PMID: 25678556; PMCID: PMC4681433.
Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Noguchi S, Agirre E, Kashi K, Samudyata, Luginbühl J, Cazzoli R, Agrawal S, Luscombe NM, Blanchette M, Kasukawa T, Hoon M, Arner E, Lenhard B, Plessy C, Castelo-Branco G, Orlando V, Carninci P. RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nat Commun. 2020 Feb 24;11(1):1018. doi: 10.1038/s41467-020-14337-6. PMID: 32094342; PMCID: PMC7039879.
Hashimoto K, Suzuki AM, Dos Santos A, Desterke C, Collino A, Ghisletti S, Braun E, Bonetti A, Fort A, Qin XY, Radaelli E, Kaczkowski B, Forrest AR, Kojima S, Samuel D, Natoli G, Buendia MA, Faivre J, Carninci P. CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors. Genome Res. 2015 Dec;25(12):1812-24. doi: 10.1101/gr.191031.115. Epub 2015 Oct 28. PMID: 26510915; PMCID: PMC4665003.
Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR; FANTOM5 Consortium. Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers. Cancer Res . 2016 Jan 15;76(2):216-26. doi: 10.1158/0008-5472.CAN-15-0484. Epub 2015 Nov 9. PMID: 26552699